This study uses structural equation modelling (SEM) to analyse the relationship between perceived accessibility, housing and transport equity and their influencing factors in Nanjing, China. It aims to address the current shortfall in studies to compare differences in perceived (rather than objective) measures of accessibility using a transport equity lens. A comparison sample of 664 affordable housing residents and 828 commercial housing residents living in different locations across the city was collected through an online survey. The research shows that affordable housing residents are in a more disadvantaged position than commercial housing residents based on their perceived accessibility, housing and transport equity evaluation results are all worse than those of commercial housing residents. Therefore, two SEM models were constructed to understand the underlying factors driving these perceptions. The results show that both housing location and transport provision significantly affect perceived accessibility, housing and transport equity. Improving people’s transport affordability is the most effective way to improve perceived accessibility, and transport equity for both groups, however, improving the housing environment is more critical for affordable housing residents, while improving housing affordability is more important for commercial housing residents.