Summary: Diatom blooms can significantly influence the dynamics of microbial communities, yet little is known about the interaction and assembly mechanisms of abundant and rare taxa during bloom process. Here, using 16S rRNA gene amplicon sequencing, we investigated the co‐occurrence patterns and assembly processes of abundant and rare microbial communities during an early spring diatom bloom in Xiangshan bay. Our results showed that α‐diversity indices in the rare subcommunity (RS) were significantly higher than those in the abundant and common subcommunities. β‐Diversity of the RS was the highest among three subcommunities, and the variation of β‐diversity in the three subcommunities was mainly induced by species turnover, which was also the highest in the RS. The assembly of microbial communities was mainly driven by the neutral processes, but the roles of neutral processes might differ in each subcommunity. Co‐occurrence network analysis revealed that abundant and common operational taxonomic units were more often located in central positions within the network. Most of the modules in the network were specific to a particular bloom stage, owing to the succession of Skeletonema costatum . Overall, these findings expand current understanding of the microbial interaction and assembly mechanisms in marine environment suffering harmful algal bloom disturbance.