Periphytic algae are important primary producers in water bodies, which play an important role in maintaining ecological function and water purification. Previous studies have shown that plastic is a good substrate for periphytic algae, and different plastic materials have different effects on the colonization of periphytic algae; however, there are few reports on the effects of plastic color on the growth of periphytic algae. In this study, polycarbonate plastic (PC) of various colors were used as the substrate to study the effects of different colors on the growth and community structure of periphytic algae by measuring the biomass, photosynthetic activity, and community composition. The results showed that the growth of periphytic algae was inhibited by the brown PC plastic, and the contents of chlorophyll a and dry weight in this group were significantly lower than those in other groups. Green PC plastic inhibited the photosynthetic activity of periphytic algae, and the actual photosynthetic efficiency (Yield) of the group was significantly lower than that of the other groups. The influence of PC plastic with different colors on periphytic algae occurred mainly in the early colonization/development stage but was not significant in the late community maturity stage. On day seven of the experiment, the community composition of periphytic algae was significantly different between the transparent PC plastic group and the green PC plastic group. By contrast, on days 25 and 40, there were no significant differences in the community structure of periphytic algae. In the early stage of the experiment, the dominant genus was Pseudoranea (Cyanophyta), and in the middle and mature stages, the dominant genus was Mougeotia (Chlorophyta). In this study, the effects of different colors of polycarbonate plastics on periphytic algae were investigated, which provided new insights for selecting suitable substrates for water pollution treatment by using periphyton biotechnology.