The 25-year-old was arrested in the border town of Nong Khai with the tubes packed inside a nitrogen tank, according to a Thai customs officer.
"It was his 13th time smuggling (semen) through Nong Khai," the official told AFP, requesting anonymity because he was not authorised to speak to the press.
Officials believe the vials were bound for a surrogacy clinic in Laos, an impoverished country that is quickly soaking up demand for the "rent a womb" business.
A number of Laos-linked surrogacy agencies and IVF clinics have cropped up in recent months, according to consultancy group Families Through Surrogacy.
Some offer services to carry out the embryo transfer in Laos and then provide pregnancy care for the surrogate in Thailand, a wealthier country with vastly superior medical facilities.
According to the Thai customs officer, the man was carrying sperm donated from Chinese and Vietnamese men in Bangkok.
Thailand for years hosted a thriving yet largely unregulated international surrogacy industry popular with same-sex couples.
But a string of scandals in 2014 - including tussles over custody - spurred the military government to bar foreigners from using Thai surrogates.
In one high-profile controversy, authorities discovered nine babies in a Bangkok apartment that had been fathered by a Japanese man using Thai surrogate mothers.
Thailand's crackdown pushed the industry over to neighbouring Cambodia, where it took off until the government banned surrogacy last year.
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