Based on panel data of 31 provinces, autonomous regions and cities in China from 2006 to 2016, this paper examines the relationship between industrial agglomeration and housing affordability. The results indicate that the imbalance in the development of the secondary industry between regions has been improved, but the regional differences in the ratio of house price to income are still more obvious. Residents in the eastern and central regions are facing greater housing pressure. There exists a significantly inversed-U relationship between industrial agglomeration and residents，housing affordability. In the early stage of industrial agglomeration, there is a significant positive relationship between housing affordability and industrial agglomeration. However, when the industrial agglomeration reaches the critical value, there is a significant negative relationship between housing affordability and the quadratic term of industrial agglomeration, and industrial agglomeration begins to counteract housing affordability. In addition, factors such as population density, employment wages and environmental pollution have a significant negative effect on housing affordability, and the increase in fixed assets investment in the energy industry can improve housing affordability.