The creatures, prized for their skin, scales and meat and hunted extensively in Southeast Asia, are believed to have originated in Malaysia or southern Thailand.
"The pangolins were on their way to Laos and then finally China," said Lieutenant Commander Garan Minwong of the Thai navy's Mekong river task force in the country's northern border area.
He said two suspects were arrested during the raid late Monday before they were able to load the live pangolins onto a boat.
Thailand, seen as a hub for traffickers of all endangered species, came under pressure over the rampant smuggling of ivory through its territory during Convention on International Trade in Endangered Species (CITES) talks in Bangkok this month.