As the most primitive germ cells in the testis, spermatogonial stem cells (SSCs) not only constantly renew themselves to ensure their quantity, but also differentiate into mature sperm cells to complete spermatogenesis and transmit genetic information to the next generation. Successful spermatogenesis is inseparable from niche regulation, which provides factors that enhance the self-renewal of SSCs to maintain their numbers and directs the appropriate differentiation of spermatogonia. Some progress has been achieved in the definition and isolation of SSCs. However, a high degree of cellular heterogeneity is found in the testis, revealing a combination of various cell types at different developmental stages and a lack of specific molecular markers (especially in domestic animals) for fully screening and purifying SSCs. These factors have considerably hindered further research into the mechanisms of maintenance, self-renewal, and differentiation of SSCs, as well as limited their isolation, purification, and applications. Accumulated studies have recently successfully employed single-cell RNA sequencing (scRNA-seq) as a novel approach to detailing the classification of cell subsets, mining specifically expressed genes in different cell types, and accurate identification of specific cell types. This review summarises the progress of SSCs identification and offers new insights into the SSCs developmental trajectory from single-cell RNA sequencing.