Investigating the diversity and structure of prokaryotic microbial communities in high-altitude salt lakes can reflect the ecological functions of these communities and their relationships with the physicochemical properties of surface sediments. This study used Illumina high-throughput sequencing technology to study 24 surface sediment samples from Lake Qinghai and Chaka. Prokaryotic microbial diversity, distribution patterns and formation mechanisms were explored through β-diversity decomposition. The influence of salinity on the diversity of prokaryotic microbial communities was further quantified using PLS-SEM, and the interspecies interactions among prokaryotic microorganisms in different salt lakes were elucidated through molecular ecological network analysis. The results showed that electrical conductivity (EC) is the most important factor affecting the distribution, abundance and diversity of prokaryotic microorganisms in Lake Qinghai and Chaka. Additionally, the study found that Proteobacteria and Bacteroidetes were the most dominant bacterial groups, while Euryarchaeota was the predominant and prevalent archaea in both lakes. Furthermore, prokaryotic microbial communities were largely contributed by the nestedness component shown in the total β-diversity analysis. Prokaryotic microbial communities showed greater positive interactions in Lake Chaka compared to Lake Qinghai, suggesting reduced niche differentiation and increased cooperation in response to high-salinity stress. Overall, this study provides new insights into the ecological strategies of prokaryotic microorganisms under salt stress conditions and helps deepen the understanding of the complex dynamics of prokaryotic microbial communities in the surface sediments of salt lakes on the Qinghai-Tibet Plateau.