Forest streams in the high-frigid areas are not only the source of water for regional rivers, but they also play important roles in the ecological linkage between land and water areas. Since relative low temperature could limit the activity and productivity of microorganisms, the organism structure in the steams is relatively homogeneous, although microbial activity could be the key ecological factor regulating the ecological processes of stream ecosystem. Moreover, the available information about the structure and the dynamic processes of the microbial community has not been sufficiently documented in the high-frigid forest streams. Therefore, the structural dynamics of microbial community were investigated both in soil and streams in a coniferous forest in western Sichuan, China. Real-time fluorescent quantitative PCR and denatured gradient gel electrophoresis (DGGE) were used. Environmental factors such as temperature, pH, dissolved organic carbon, dissolved oxygen, and stream water conductivity were also monitored at different seasonal stages in the freezing-thawing and the growing seasons from 2014 to 2015. The results showed that the microbial abundance observed in streams was relatively lower than that in soil at each key period throughout the year. The ratio of fungi to bacteria was higher in winter than in the growing season in both streams and soil. The microbial abundance and community diversity showed similar dynamic patterns both in streams and soil. In contrast, the peak of microbial abundance and Shannon-Wiener diversity index in streams appeared in the growing season, whereas in soil, this was in the winter. Moreover, there were significant differences in the bacterial abundance in each key period in streams. Furthermore, the results from sequencing analysis revealed that the main bacterial species in streams was Rhodococcus sp., but in soil, it was Bacillus sp. The main fungal species in streams were Aspergillus sp. and Cenococcum sp., whereas Pleosporales sp., Aspergillus sp. and some other Ascomycota were the main ones in soil. In addition, the environmental heterogeneity, seasonal changes, and microenvironmental factors (e.g., temperature, pH, and nutrient availability such as dissolved organic carbon and dissolved oxygen) showed substantial effects on microbial community structure and composition in streams in the high-frigid forest.