Although the top-down and bottom-up concept in microbial food-webs has been a primary interest in ecology, less is still known about it in soil ecosystems. Protists are the primary top-down predators of bacterial communities, altering their compositions, while the bottom-up resources are the primary factors limiting bacterial growth. Here, we hypothesized that the top-down predators modulate soil bacterial community composition, while the bottom-up nutrients control the bacterial growth and population. To precisely control nutrient levels, we used an inert soil substitute consisting of a combination of calcined clay and sand. Nutrients equivalent to the reference paddy field soil were added to microcosms as a control treatment. To investigate the effects of C, N, and P, six additional bottom-up treatments in the absence and double amounts of the nutrients were prepared. Four top-down treatments (no protist addition, Acanthamoeba castellanii, Vermamoeba vermiformis, and Heteromita globosa) were set up for each bottom-up treatment. A total of 252 microcosms under 28 treatments were incubated. Bacterial communities were analyzed using high-throughput sequencing and real-time PCR in the 1st, 3rd, and 5th weeks. The results revealed that the top-down predators significantly altered the bacterial community composition, and the bacterial population was predominantly controlled by the bottom-up nutrients. Analysis of absolute abundance data demonstrated that both top-down and bottom-up factors shaped the bacterial community structure (community composition and population). Random forest analysis classified the amplicon sequence variants associated with the treatments, showing that mostly similar families were affected by both bottom-up and top-down factors. In conclusion, the results of this study fully supported our hypothesis that top-down predators alter community composition, while bottom-up factors influence bacterial population dynamics.