SITE 7, Thailand (AP) _ Tens of thousands of Cambodian refugees greeted U.S. Secretary of State George P. Shultz when he helicoptered Tuesday to the Thai-Cambodian border to show support for Thailand and its non-communist allies.

Chanting, ''USA - No. 1,'' and ''We want to go home,'' virtually all of the 53,285 refugees living at Site 7 on the border turned out for his arrival.

Shultz, the highest-ranking American to visit the frontier, listened to refugees' stories of alleged atrocities committed by Vietnamese troops in Cambodia as he toured the site.

The refugees displayed a large white banner which read: ''We have manpower. We need arms and education. U.S. AID, please help us turn Vietnamese killing fields to Cambodian farming fields. We want to go home. God bless America.''

Other placards, all in English, asked for weapons and said Shultz' visit gave the refugees hope.

Shultz is to travel by helicopter along the border where he will tour a refugee processing center, a refugee camp and frontline Thai positions.

Shultz arrived at the frontier from Bangkok where he Monday condemned the Vietnamese military presence in Cambodia and the suffering he said it had brought along the Thai-Cambodian frontier.

''I know you're all very well aware of the strategic and political implications of the Vietnamese occupation of Cambodia, and you are also aware of the Soviet support that makes it possible,'' he said on his arrival in Thailand for a week-long visit to Southeast Asia. ''You know also of its arrogant and illegal nature.''

Shultz later met with Thailand's Prime Minister Prem Tinsulanonda, acting Foreign Minister Praphas Limpabandhu, several top economic officials and three leaders of non-communist Cambodian resistance groups.

A State Department official travelling with Shultz declined comment on a Washington Post report Monday that said the CIA has provided ''non-lethal'' aid to two of the non-communist groups since 1982.

The United States provides about $16 million annually to the international effort to aid Cambodian refugees along the border. A bill before Congress would funnel $5 million in economic aid to the non-communist guerrilla groups allied with the communist Khmer Rouge in a coalition government in exile.

Prem expressed appreciation for Washington's aid to Thailand, which has included accelerated weapons deliveries, diplomatic backing and a letter from President Reagan during Vietnam's border offensive last April. Thai and Vietnamese forces have clashed more than 20 times along the border since last November, and the Foreign Ministry says 101 Thais were killed in the fighting.

Shultz took a tough' position regarding Vietnamese troops in Cambodia even though Vietnam announced it would hand over the remains of 26 Americans killed in the Vietnam War.

He told Prem that Washington regards the issue of the missing American servicemen as separate from other problems with Vietnam, according to a state department official. The official could not be identified by name under the rules of the briefing.

In Washington, State Department spokesman Edward Djerejian said the United States was ''very pleased'' at Vietnam's promise to transfer the remains, and appreciates the ''concrete demonstration'' of its commitment to resolve the issue.

Shultz is expected to support proposals under discussion by foreign ministers of the Association of Southeast Asian Nations to negotiate a settlement to the Vietnamese intervention in Cambodia. The ASEAN ministers will end a two-day conference in Kuala Lumpur on Tuesday. Shultz will fly there Wednesday for talks with the ASEAN members.

The ASEAN nations are Thailand, Indonesia, Malaysia, Singapore, the Philippines and Brunei.

The only significant difference that emerged between the Thai and U.S. officials was trade, the State Department official said.

He said the Thais were ''extremely nervous'' about U.S. protectionism and expressed appreciation for the Reagan administration's efforts to blunt such moves in Congress.

Finance Minister Sommai Hoontrakul told reporters that the Shultz group was given a 12-page letter asking for the Reagan Administration's help in solving bilateral trade problems.

U.S. statistics show the United States had a $300 million trade deficit with Thailand last year. The Thais are fearful a bill now before Congress would drastically cut their exports of textile to the United States.