Thylakoids are the important sites where photosynthesis takes place. The thylakoid membrane envelops a central aqueous region known as the thylakoid lumen. There are various types of proteins residing in thylakoid lumen including high chlorophyll fluorescence (HCF) protein, immunophilins, oxygen-evolving complex (OEC) proteins, PsbP-like proteins, etc. These proteins were considered to play important roles during various physiological processes, such as photosynthesis, nucleotide metabolism and redox regulation. This review systematically summarizes the function of thylakoid lumen proteins involved in photosynthesis regulation, such as photosystem assembly, growth regulation and excess light stress response, and provides the theoretical reference for future study on the physiological function of thylakoid lumen proteins.