The effects of seed soaking agent prochloraz on the structure of microbial community in rice seeds were studied by setting seed soaking with water （CK） and seed soaking with prochloraz （Soak）, 16S rRNA amplicon sequencing and isolation culture methods in conventional japonica rice Xiushui 134. The results showed that compared with CK, the number of fungi on rice seed surface of Soak was significantly reduced. However, Soak had no significant effect on the diversity and composition of bacterial communities in rice seeds, including Shannon index, Chao1 index, Observed OTUs, β diversity and relative abundance of dominant bacteria. Thus, in agricultural production, prochloraz soaking as a measure to control rice seed-borne diseases has no significant effect on seed endophytic bacteria.