Based on the super-efficiency SBM-DEA model of non-expected output, the innovation efficiency of green transportation technology in 16 cities of Chengdu-Chongqing urban agglomeration from 2001 to 2020 was measured, and the panel Tobit model was used to analyze its influencing factors. The results show that the innovation efficiency of green transportation technology in Chengdu-Chongqing urban agglomeration fluctuates at a low level from 2001 to 2012, and increases at a higher rate from 2013 to 2020. In 2020, an obvious “center-periphery” spatial distribution pattern of green transportation technology innovation efficiency is formed along the Chengdu-Chongqing dual-core development main axis, but the gap between cities is still obvious. According to the regression results of panel Tobit model, transport industry location entropy, the number of researchers, environmental regulation intensity all have significant promoting effects on the innovation efficiency of green transport technology in Chengdu-Chongqing urban agglomeration.