Previous studies have shown that PRSS55 is required for male fertility in mice, and potentially in humans, and is involved in energy metabolism in mouse sperm. However, the underline mechanism remains unclear. Here we show that Prss55 deficiency leads to significant changes in protein levels identified by DIA-based mass spectrometry proteomics in enriched PRSS55-expressing testicular cells and caudal epididymal sperm as compared to wt mice. Bioinformatic assessments reveal that the majority of differentially expressed proteins (DEPs) were significantly enriched in the branched-chain amino acids (BCAA) degradation pathway and the oxidative phosphorylation (OXPHOS) process. Accumulation of isoleucine and leucine was identified in Prss55-/- mice by untargeted metabolomics. We also observe significantly downregulated IVD and NDUFB8 protein levels, impaired in adenosine triphosphate (ATP) production, abnormal NAD+/NADH ratio, and decreased mitochondrial membrane potential in knockout models. Secondly, co-immunoprecipitation/mass spectrometry (Co-IP/MS) by using V5-PRSS55 knock-in mice and in vitro Co-IP assays suggested that PRSS55 interacts with mitochondrial protein BCKDK, which is involved in BCAA metabolism. Overexpressed PRSS55 was found to be enriched in mitochondria by immunofluorescence and immunoblotting assays. All these data demonstrate that PRSS55 regulates energy homeostasis and BCAAs metabolism in testes and sperm of mice, implicating a potential mechanism of male infertility in mice lacking PRSS55 and in human due to PRSS55 mutation.