The control of taste and odor (T&O) in drinking water reservoirs is the main challenge for water supply. T&O is mainly derived from actinobacteria during non-algal blooms. However, few studies have investigated the actinobacterial community in reservoirs, especially the effects of water quality parameters on actinobacteria. This study analyzed the environmental driving force of the actinobacterial community composition and change in time and space through structural equations and network in drinking water reservoirs. The results showed a high abundance of actinobacteria, up to 2.7 × 104 actinobacteria per 1 L, in the hypolimnion of the Lijiahe reservoir in September, which is one order of magnitude greater than that in the Jinpen reservoir. The two drinking water reservoirs had similar dominant genera, mainly Sporichthya sp., and Mycobacterium sp., and difference in the actinobacterial proportions. However, there was a large difference at the dominant species. Rhodococcus fascians (4.02%) was the dominant species in the Lijiahe reservoir, while Mycobacterium chlorophenolicum (6.64%) was the dominant species in the Jinpen reservoir. Network analysis revealed that the structure of the network in the Lijiahe reservoir was more unstable; thus, it was vulnerable to environmental disturbances. In addition, a low abundance of species may play a critical role in the actinobacterial community structure of aquatic ecosystems. Structural equation modeling analysis suggested that water temperature, dissolved oxygen, and nutrition were the dominant factors affecting the abundance and community of actinobacteria. Overall, these findings broaden the understanding of the distribution and co-existence of actinobacterial communities in drinking water reservoirs and provide valuable clues for the biological controls of T&O and reservoir management.