The objective of this study was to determine the impact of high hydrostatic pressure (HHP) treatment on microbial communities in Chinese water-boiled salted duck (CWBSD) and the synergistic effect of HHP and mild heat treatment. In this work, the bacterial diversity was evaluated by using both a culture-dependent method and denaturing gradient gel electrophoresis. The total aerobic bacterial counts in pressure-treated samples were significantly lower than those in controls, which indicated that HHP could extend the shelf life of CWBSD. Weissella hellenica and Enterobacteriaceae, the predominant bacteria found in CWBSD, were not detected after HHP treatment. On the other hand, Staphylococcus spp. and Bacillus spp. became the predominant bacteria in HHP-treated samples. Moreover, the inhibitory effect was greater at 400 MPa than at 200 MPa combined with mild heat at 40°C. This study investigated the diversity of bacteria in HHP-treated CWBSD, and the information derived from this research may help to understand the bacterial ecology and develop effective HHP treatments to extend the shelf life of CWBSD.