Based on the micro-data of new manufacturing firms in the Yangtze River Delta from 2005 to 2013, using the discrete choice model to examine the effects of firm heterogeneity on location choice, and analyzing the spatial distribution of firms with different characteristics. From the perspective of firm heterogeneity, the influencing mechanism of location choice of new manufacturing firms in China is explained. The results show that the role of location factors is different among different firms, and the influence of firm heterogeneity on location selection is varied. As the number of employees increases, new manufacturing firms tend to choose middle-level cities and are less likely to choose sites in developed cities with fierce competition. State-owned ownership has no significant influence on the location choice, while foreign-invested firms prefer more developed cities where existing foreign manufacturing firms are concentrated. Similar to foreign-invested enterprises, high-tech manufacturing firms also have obvious characteristics of geographical clustering.