Rice is one of the most important crops in China. Rice root morphology and root activity are closely associated with the growth and development of above-ground part of plant. Soil microorganisms, acting as the catalyzer of matter cycle in soil, mediate the supplement of soil nutrients to rice root, which are significant to the growth and development of rice roots. In this review, the effects of bacteria, fungi and actinomycetes in soil microorganism on rice root morphology and root activity were summarized. The research idea of the relationship between soil microorganisms and rice roots was put forward in order to lay a theoretical basis for improving the morphological and physiological characteristics of rice roots, and high yielding in rice cultivation.