Phytoplankton mainly capture solar energy by chlorophyll-based photosystems, which can be inhibited by nutrient stress. Besides photosynthesis, proton pump rhodopsin (PPR) is also a major solar sink in marine ecosystem, which can convert solar energy into chemical energy for supporting basal metabolism under carbon or nutrients-limited condition. The PPR abundance was supposed to be influenced by nutrient content in the surface ocean, but the association of PPR with phosphorus nutrition is not quite clear and warrants further studies. Here, we report a microbial rhodopsin discovered in B. minutum (BmR). Both phylogenetic analysis and structure prediction results indicate that BmR is similar to those of known eukaryotic proton pump rhodopsins and should be a Xanthorhodopsins-like rhodopsin. In worldwide scope, BmR distributed widely and its expression can be stimulated by environmental nutrients parameters, including phosphorus. To further study BmR’s response to phosphorus limitation, we cultured B. minutum under different phosphorus conditions. Phosphorus limitation conditions led to changes in physiological parameters of B. minutum, including cell growth, photosynthesis efficiency, carbon and nitrogen fixation, and so on. All changes in physiological parameters confirmed that B. minutum’s photosynthesis is constricted under real phosphorus limitation condition. Meanwhile, the rhodopsin of B. minutum (BmR) is strong upregulated under phosphorus limitation condition. Furthermore, strong positive correlations with cellular Chl a and alkaline phosphatase activity and a negative correlation with Fv/Fm were observed. Therefore, the study highlights that BmR possibly provides supplementary energy to support cell basal metabolisms when photosynthesis of B. minutum is impaired by phosphorus limitation condition.