Topmouth culter (Culter alburnus) is a large Cyprinidae fish, which occupies the top of the food chain in freshwater ecosystems and has a crucial contribution to the stability of aquatic ecosystems. Due to human activities, this species is facing the challenges of reduced natural resources and decreased genetic diversity within its population. Genetic diversity has direct impacts on growth, survival, and reproductive capabilities of fish. However, current genetic research on the cultured populations of C. alburnus is still insufficient. The importance of genetic resource conservation has not yet been fully recognized. In this study, whole genome resequencing (WGS) was used to conduct a comprehensive analysis of three cultured populations of C. alburnus from Taihu (TH), Qingyuan (QY), and Yangzhou (YZ) regions in order to evaluate the population genetic diversity level in these three regions, explore their genetic characteristics, and investigate the genetic differences among them. A total of 23156699 SNPs were identified, and SNP variants were mainly located in intergenic (47.21%) and intron (39.37%) regions. SNP markers in all three populations showed low polymorphism (PIC value ＜0.25). The TH population (0.1923) had the highest inbreeding coefficient, indicating a much higher degree of inbreeding than the QY (0.0631) and YZ (–0.0280) populations. Population structure analysis revealed that each of the three populations clustered into a branch; the TH population was separated into a distinct cluster derived from the common ancestor, whereas the QY and YZ populations may have been genetically influenced by multiple ancestral populations. The LD decay plot demonstrated that the TH population had the largest decay distance and slowest decay rate, whereas the YZ population showed a lower degree of linkage disequilibrium. Both genetic differentiation index (F_st) and gene flow (N_m) indicated that there was a certain degree of genetic differentiation among the three populations, and that the TH population was significantly differentiated from the other populations. Through selective scanning analysis based on nucleotide diversity (π) and fixation index of population genetic differentiation (F_st), with the QY and YZ populations as reference groups, a total of 572 and 602 selective genes were identified in the TH population, respectively. These genes are involved in biological processes such as energy metabolism, oxidative stress response, and inflammatory response. Selective signal detection results indicated that the most selected regions were located on chromosomes 3 and 7. Furthermore, the YZ population exhibited relatively high genetic diversity and showed a lower degree of domestication, whereas the TH population displayed the lowest genetic diversity and was strongly influenced by artificial selection. Our research provides basic data support for genetic studies and germplasm conservation management of C. alburnus cultured populations. This not only provides a reference for developing breeding selection strategies but also can help to formulate effective genetic resource conservation and culture management strategies.