Microalgae biofilm-based culture systems have received considerable attention because their water requirements and harvesting costs are lower, and biomass productivity is higher, than in suspended culture systems. The photosynthetic properties and microstructure of microalgae biofilms have fundamental effects on biofilm growth. We investigated the photosynthetic parameters, microstructures, biomass accumulation, and CO2 fixation rate of Chlorella sp. biofilms cultured under a series of light intensities (20, 50, 100, 200, and 400 μmol·m−2·s−1). The results indicated that microalgae biofilms had higher photosynthetic potentials and more porous microstructures under low light intensities, and that both of these promoted the efficiency of photon use. In contrast, biofilms under high light intensities exhibited higher photo-protection capabilities and more compact microstructures, which protected microalgae against photo damage. The study revealed that microalgae biofilms have excellent self-adaption capabilities to cope with varying light intensities, and these have significant implications for selection of the optimal light intensity when designing more efficient biofilm-based microalgae culture systems.