Prognosis and diagnosis of male fertility is a most important for animal breeding system and human reproduction. Conventional semen analysis generally provides information on the quantitative parameters of spermatozoa, but yields no information concerning its functional competence. Thus, new methods for diagnosis and prognosis of male fertility will need to be developed to ensure more accurate assessments. Proteomics have used to find candidate biomarkers for male fertility, but the relationship between the proteome and fertility was not fully understood. Therefore, we performed a comprehensive proteomic approach to investigate small and large litter size boar spermatozoa and identify proteins related to negative male fertility. In present study, 20 proteins showed differential expression levels in small and large litter size groups. Nineteen of these proteins were abundantly expressed in the small litter group. Interestingly, only one protein was highly expressed in the large litter size spermatozoa. We then identified signaling pathways associated with the differentially expressed protein markers. Glutathione S-transferase Mu3 and glutathione peroxidase 4 were related to the glutathione metabolic pathway and arginine vasopressin receptor 2 was linked to vasopressin R2/STAT. Taken together, our results suggest that identified negative fertility-related biomarkers may be used as negative biomarkers for the detection of inferior male fertility such as sub-fertility or infertility.