Both microplastics and persistent organic pollutants (POPs) are ubiquitously present in natural water environment, posing a potential threat to aquatic organisms. While it has been suggested that the immune responses of aquatic organisms could be hampered by exposure to microplastics and POPs, the synergistic immunotoxic impact of these two types of pollutants remain poorly understood. In addition, little is known about the mechanism behind the immunotoxic effect of microplastics. Therefore, in the present study, the immunotoxicity of microplastics and two POPs, benzo[a]pyrene (B[a]P) and 17β-estradiol (E2), were investigated alone or in combination in a bivalve species, Tegillarca granosa. Evident immunotoxicity, as indicated by alterations of haemocyte count, blood cell composition, phagocytic activity, intracellular content of ROS, concentration of Ca and lysozyme, and lysozyme activity, was revealed for both microplastics and the two POPs examined. In addition, the expression of six immune-, Ca signalling-, and apoptosis-related genes was significantly altered by exposure of clams to the contaminants studied. Furthermore, the toxicity of POPs was generally aggravated by smaller microplastics (500 nm) and mitigated by larger ones (30 μm). This size dependent effect on POP toxicity may result from size dependent interactions between microplastics and POPs. Data obtained in this study also indicate that similar to exposure to B[a]P and E2, exposure to microplastics may hamper the immune responses of clams through a series of interdependent physiological and molecular processes.