Optogenetics is an emerging technique that exploits light to control cells by combining optics and genetics techniques. In optogenetic systems, cells are genetically modified to express photosensitive proteins and consequently become responsive to light pulses. Optogenetics has revolutionized neuroscience research by facilitating selective and rapid control of targeted neurons expressing light-gated ion channels. In addition to light-gated ion channels, photosensitive proteins based on light-gated protein-protein interactions are widely used in optogenetic research. In this review, we discuss these common photosensitive proteins and summarize optogenetic applications in optical control of gene expression, phase separation, biosynthesis, and organelle distribution based on light-gated protein-protein interactions.