Dejan Gluscevic's boys were outclassed by a dominant home side as they got off to a poor start
The hosts largely dominated throughout and got off to a good start when Issariya Marom put them ahead in the 11th minute. The midfielder doubled his tally in first-half injury time with another goal in the 47th minute.
Dejan Gluscevic's boys only threatened once through Illyas Lee before the break, and striker Chenrop Samphaodi sealed the win in the 56th minute as the Thais left the Thai-Japanese Stadium victorious.
But Somchai Chuayboonchum's team are only second in the four-man group after North Korea thrashed Brunei 6-0 in the other Group H game to sit pretty at the top.
The Singapore U19s came into this tournament on the back of a poor showing at the AFF U19 Championship last month, where they crashed out at the group stages after losing to the likes of Laos and Cambodia.
They have two more matches to fight for qualification, with the next game against North Korea on Thursday at 3p.m.