Flex-route transit (FRT) has significant advantages in low-demand areas. Existing studies have focused on practical experience, strategic planning, and operational planning. Few studies have addressed the effect of sociodemographic and psychological latent characteristics on the acceptance of FRT. This study aims at exploring the effect of sociodemographic and psychological latent characteristics on FRT acceptance. To finish the goal, a household survey is conducted from April to May 2020 in Nanjing, China. The survey includes sociodemographic characteristics and observed variables of individuals. Firstly, the study extracts six psychological latent characteristics to reflect individuals’ attitudes based on previous and mature researches in the field of technology acceptance model (TAM) and theory of planned behavior (TPB). Then, a multiple indicators and multiple causes (MIMIC) is applied to calculate six psychological latent characteristics. Finally, an integrated model, consisting of the MIMIC and a binary logit model (BLM), is applied to match sociodemographic and psychological latent characteristics. The BLM with sociodemographic characteristics is developed as the reference model to compare the effects of psychological latent characteristics. Results show that psychological latent factors play a significant role in estimating the effect on FRT acceptance. Results of the integrated model show that the parameter of car is -0.325, displaying individuals with private cars are more reluctant to use FRT. Therefore, restricting private cars is an effective measure to facilitate FRT. Improving flexibility (0.241) is a significant measure to facilitate FRT. Findings are expected to facilitate decision-making of transport planners and engineers, and therefore enhance the service of the FRT system.