Facilitated by the high-throughput sequencing (HTS) technique, the importance of protists to aquatic systems has been widely acknowledged in the last decade. However, information of protistan biotic interactions and seasonal dynamics is much less known in the coast ecosystem with intensive anthropic disturbance. In this study, year-round changes of protist community composition and diversity in the coastal water of Yantai, a city along the northern Yellow Sea in China, were investigated using HTS for the V4 region of 18S rDNA. The interactions among protist groups were also analyzed using the co-occurrence network. Data analyses showed that Alveolata, Chlorophyta, and Stramenopiles are the most dominant phytoplanktonic protists in the investigated coastal area. The community composition displayed strong seasonal variation. The abundant families Dino-Group-I-Clade-1 and Ulotrichales_ X had higher proportions in spring and summer, while Bathycoccaceae exhibited higher ratios in autumn and winter. Alpha diversities (Shannon and Simpson) were the highest in autumn and the lowest in spring (ANOVA test, P < 0.05). Nutrients (SiO 4 2-, PO 4 3-), total organic carbon (TOC), and pH seemed to drive the variation of alpha diversity, while temperature, PO 4 3- and TON were the most significant factors influencing the whole protist community. Co-variance network analyses reveal frequent co-occurrence events among ciliates, chlorophytes and dinoflagellate, suggesting biotic interactions have been induced by predation, parasitism and mixotrophy.