Public transport ridership has been hit hard by the COVID-19 pandemic in many countries. Investigating passengers' public transport mode choice behavior during large-scale public health incidents can uncover the major influential factors and help propose policies and strategies to reduce the pandemic transmission and recover the public transport revenue. This study develops an integrated choice and latent variables (ICLV) model by income based on structural equation model to model passengers' public transport choice behavior during the normalized stage of the pandemic. The model considers passengers' socioeconomic attributes, travel attributes, and attitude-perception attributes, and can appropriately capture passengers' psychological latent attributes. Taking Beijing China as an example, we collect some revealed preference survey data online. The modeling results show that the risk perception as a mediator variable has a significant impact on mode preference. Moreover, the convenience of public transport has the largest influence on risk perception. These findings suggest that risk perception and the convenience of public transport play a major role in passengers' mode choice behavior. In addition, the impacts of the various influential factors on the public transport mode choices are significantly different across different income groups. Further, the ICLV model can achieve better performance and is superior to the traditional Multinomial Logit model. The modeling framework can help propose targeted and instructive strategies during the normalized stage of the pandemic by uncovering the major influential factors in passengers’ public transport mode choices, which is applicable to similar pandemics in the future.