In order to study the effect of high hydrostatic pressure （HHP） on the changes of bacterial community structure in perch （Lateolabrax japonicus） fillets under cold storage， one of the samples were treated at 250 MPa for 9 min （HHP group） and the other one were treated at 0.1 MPa （CK group）. Then samples in two groups can be stored at 4 ℃， total volatile basic nitrogen（TVB-N） and microbial indexes （total viable counts （TVC）， Shewanella counts， Pseudomonas counts and Psychrobacter bacteria counts （PBC）） were measured at day 0， 3， 6， 9， 11， 13 and 15 respectively. The correlation was analyzed at the same time so as to evaluate the effect of HHP in the quality of perch （Lateolabrax japonicus） fillets under cold storage. The bacterial community structure of perch （Lateolabrax japonicus） fillets at different storage time （early， middle， later and final stages） was carried out by high throughput sequencing technology. The results showed that the increase of TVB-N， TVC， Shewanella counts， Pseudomonas counts and PBC were significantly slower than that of control group. TVB-N value and microbial indexes can be used as freshness evaluation indexes for analyzing the quality changes of （Lateolabrax japonicus） fillets after HHP treatment. The results of high throughput sequencing indicated that the main bacteria in CK and HHP group were Bacillus sp.， Bacillus subtilis sp. and Lactococcus sp.， but the composition and type of bacteria between two groups at the later of storage were shown at the significant difference. The main bacteria of CK group in the later of storage was Pseudomonas sp. and that of HHP group was Psychobacter sp. The main bacteria of CK group in final storage was Psychobacter sp.， Pseudomonas sp. Shewanella sp. and Aeromonas sp. and that of HHP group was Psychobacter sp.， Pseudomonas sp. and Yersinia sp. HHP can inhibit the increase of TVB-N value and microbial indexes， which also have the significant effect on the bacterial composition during storage. Moreover， HHP can also significantly inhibit the growth of Psychobacter sp. and Shewanella sp.