To reveal the structural composition and temporal variation of the ciliate community on a long-term scale, the species composition, abundance and carbon biomass, as well as interactions with environmental factors, were investigated combining the data from two monitoring programs at Helgoland Roads. A total of 89 ciliate taxa representing 46 different genera were identified during the monitoring periods. The ciliate community was dominated by aloricate oligotrichs and the photosynthesis-performing ciliates Mesodinium rubrum and Mesodinium major in terms of abundance and carbon biomass and exhibited clear seasonal patterns, with high values in spring and summer and low values in autumn and winter and a distinct peak in June mainly due to the bloom of M. rubrum and M. major. Univariate correlation analyses were conducted using the ciliate data from two monitoring programs and the environmental parameters from the Helgoland Roads long-term date set. The results showed that the ciliate community was positively correlated with water temperature and Chlorophyll a and negatively correlated with various inorganic nutrients, and was strongly influenced by the food availability. Multivariate analyses revealed that the ciliate community exhibited not only seasonal variation at a short-term scale but also annual variation at a long-term scale in terms of community structure, dominant species and influencing factors. The results from both univariate and multivariate analyses indicate that water temperature and various inorganic nutrients might not directly control the temporal dynamics of the ciliate community but indirectly influence it via the food availability. This study is the first detailed investigation on the ciliate community in the North Sea regarding the structural composition and temporal variation in relation to environmental factors. Our findings suggest that long-term monitoring programs on the ciliate community as a crucial food web component are essential.