Biochar-modified polyacrylate-like polymers are promising waterborne polymer-based membrane coatings for controlled-release fertilizers. However, the effect of these membrane polymers on paddy soil is unknown. A soil incubation experiment was conducted using Fourier transform infrared photoacoustic spectroscopy to monitor the changes in the polymer-coated membranes in paddy soil, and Biolog EcoPlates and polymerase chain reaction-denaturing gradient gel electrophoresis were used to detect the effects of the membranes on soil bacterial community profiles. Compared to unmodified membranes, the biodegradation rate of the biochar-modified membrane was slower, and the membrane was more intact, which improved and guaranteed the controlled release of nutrients. Compared to the soil without membranes, the biochar-modified membranes, as well as unmodified ones, showed no significant impacts on the composition diversity of soil dominant bacterial community. The activity and functional diversity of soil culturable microbial community during the early stage of incubation were reduced by biochar-modified membranes due to the release of small amount of soluble organic materials but were both recovered in the 12(th) month of the incubation period. Therefore, the biochar-modified waterborne polyacrylate was environmentally friendly, demonstrating its potential both in the development of coated controlled-release fertilizers and in the utilization of crop residue.