The large discharge of ballast sediment of entering ships is one of the important reasons for the frequent occurrence of algae red tide disasters in China. Salinity is an important environmental factor affecting algal growth. In this study, the salinity tolerance of Cyclotella cryptica which was isolated from the sediment of the entering ship was observed in the cell density, photosynthetic efficiency and symbiotic bacteria in salinity 0, 5, 10, 15, 20, 25 and 30 culturing medium. The results showed that C. cryptica could grow in the salinity range of 0–30, with high cell density under salinity 20 and 25, low cell density under salinity 5 and 10, and photosynthetic efficiency decreased with the increase of salinity. In this experiment, C. cryptica symbiotic bacteria were detected under different salinity conditions, and the relative abundance of Marinobacter, Limnobacter, Celeribacter, unclassified Bacteroidetes, and unclassified Rhodobacteriaceae were high. Seobacterium genus showed higher abundance at salinity 10, 15, 20, 25, 30 and lower abundance at salinity 0 and 5. The genus showed higher abundance at salinity 0 and lower abundance at other salinities. Tachyophyacter showed a higher abundance at salinity 5, 10 and a lower abundance under other salinity conditions. Unclassified Bacteroidetes showed higher abundance at salinity 0, 5, 10, 15, 20 and 25 and lower abundance at salinity 30. Unclassified Rhothrobacteriaceae showed higher abundance at salinity 30 and lower abundance at salinity 0, 5, 10, 15, 20, and 25. Through a variety of complex effects, symbiont bacteria show differences in cell density and photosynthetic rate under different salinity. In this study, by studying the growth changes of C. cryptica and its symbiotic bacteria under different salinity conditions, we can provide theoretical basis and data support for the prevention and control of C. cryptica in the sediment of ballast tanks of imported ships.