The Qijiang River is a typical cascade-developed tributary in the upper Yangtze River, where successive dams have reshaped longitudinal river connectivity, yet empirical evidence remains limited regarding their effects on the population genetic patterns of small resident fishes. In this study, Saurogobio punctatus was selected as the target species, and concatenated mitochondrial cytochrome b (Cyt b), cytochrome oxidase subunit I (CO I), and control region (D-loop) sequences from nine geographical populations were analyzed to characterize the genetic diversity and genetic structure of this species under the barrier effects of cascade dams. The results showed that: (1) A total of 36 variant sites and 18 haplotypes were identified from 185 individuals, and the overall haplotype diversity and nucleotide diversity were 0.787 ± 0.019 and 0.0020 ± 0.0002, respectively. No regular pattern of genetic diversity variation was observed among populations from different river sections. (2) Analysis of the genetic differentiation index (Fst) and gene flow (Nm) indicated moderate to high genetic differentiation between the uppermost S9 population and all other populations, although some degree of gene exchange was still maintained. (3) The Analysis of Molecular Variance (AMOVA) showed that only 1.72% of the molecular variation occurred among populations, whereas 98.28% occurred within populations, and neither the haplotype phylogenetic trees nor the haplotype network exhibited obvious signatures of dam-induced isolation. (4) Mismatch distribution and neutrality tests detected no clear signal of population expansion in either the total population or populations from different river sections. Taken together, these results indicate that the cascade dams in the Qijiang River have not yet caused a significant decline in the overall genetic diversity of S. punctatus and have had only limited effects on its overall genetic structure. However, a certain degree of local differentiation has emerged in the uppermost population, suggesting that this species can still maintain relatively stable population connectivity over the short term under conditions of high-density cascade damming. This study provides basic data and scientific support for research on population genetic differentiation of small omnivorous fishes under cascade hydropower development.