Sperm development is critical for male reproductive capability; any disruption during the process of spermatogenesis will result in male infertility. In this research, we used the C‐Nap1 encoded by the gene of Cep250 knockout mouse line as the model to evaluate the impact of absent C‐Nap1 on spermatogenesis. To investigate the interaction between C‐Nap1 and spermatogenesis, we utilized single‐cell RNA sequencing to analyze 10,332 C‐Nap1+/+ and 13,308 C‐Nap1−/− testicular cells. We identified five main cell types within seminiferous tubules, including spermatogonia, Sertoli cells, spermatogonia stem cells, Leydig cells, and spermatocytes. We found a critical reduction in testicular spermatogonia and spermatocytes in C‐Nap1‐null testes, compared to its C‐Nap1+/+ controls. By combining uniform manifold approximation and projection clustering and psedotime ordering, we distinguished five spermatogonial stages/subtypes, demonstrating that type B spermatogonia differentiation and meiotic initiation are impaired during C‐Nap1‐null spermatogenesis. Following gene ontology enrichment analysis, meiosis‐specific genes downregulated in the C‐Nap1−/− testicular cells were further verified by reverse transcription polymerase chain reaction (RT‐PCR). Based on the differential gene expression, certain downregulated genes such as Ctnnb1 and Aurka encoding C‐Nap1‐binding potential β‐Catenin and Aurka are encountered, which may account for defective type B spermatogonia differentiation and meiotic entry in C‐Nap1‐null testes.