The resignation letter was submitted to the secretary-general of the Senate, acting as secretary-general of the NLA.
Gen Thawatchai was 57th on the list of 200 members of the NLA announced by the National Council for Peace and Order (NCPO) on Friday.
He resigned after it was found that he was not qualified since Section 8 (1) of the interim constitution of 2014 states that an NLA member must not have held a post in a political party during the past three years. Gen Thawatchai was a deputy leader of the Chart Pattana Party until early this year.
Gen Thawatchai said he was not sorry about missing the opportunity to sit on the NLA. He could still do something else for the country.
He voiced hois personal support for Gen Prayuth Chan-ocha, chief of the army and the NCPO chief, to take the post of prime minister in the cabinet yet to be set up.
Chularatchamontri Aziz Pitukkumpol, the leader of the Muslim religion in Thailand, has also declined a seat on tjhe NLA, saying it conflicts with his current role. Mr Aziz sent a letter to the NCPO on Friday saying he would not accept the appointment.