Heavy metal pollution in paddy soil not only affects the yield and quality of rice, but also affects the microorganisms and enzyme activities in paddy soil. This paper systematically summarized the sources of heavy metal pollution in paddy soil, the effects of heavy metal pollution on the biomass, population quantity and community structure of microorganisms, and the activities of soil enzymes, and put forward the focus and direction of the future research in view of the research shortage on the microecological effects of heavy metal pollution on paddy soil which include:1) strengthen the research on the interaction and mutual influence of rice, heavy metals and microorganisms; 2) on the basis of studying the relationship between heavy metal pollution and soil microbial ecological characteristics of paddy soil, strengthening the comprehensive and quantitative analysis of heavy metals, soil physiochemical properties and rice and other factors will be key to clarify the effects of heavy metals on soil microbial ecological characteristics and related mechanisms; 3) Applying molecular biology and systems biology methods to promote the evolution and adaptation processes of microbial activity and function in paddy soil under heavy metal pollution stress; 4) Enhance the research based on long-term localization experiments to understand the evolution law and mechanism of paddy soil ecosystem under heavy metal stress on a longer time scale and a larger spatial scale; 5) The study on the effect of heavy metal pollution on the enzyme activity of paddy soil should focus on the mechanism and the combination of kinetic and thermodynamic parameters of soil enzymes in order to deepen the interaction mechanism between soil enzymes and compound pollution, and further reveal the toxic pathway and mechanism of compound pollution, meanwhile, with the aid of molecular techniques, explore the characteristics of more undiscovered enzymes in heavy metal polluted paddy soil, and find more sensitive and widely applicable comprehensive indexes of heavy metal polluted paddy soil in order to provide scientific basis for risk assessment and bioremediation of heavy metal polluted paddy soil.