Carbon (C) plays an important role in the activity and diFversity of soil microbial community, but there is still limited information about how C source utilization soil microbial structure responds to soil organic carbon changes under the double‐cropping rice (Oryza sativa L.) system in southern China's paddy fields. Therefore, the effects of short‐term (5‐year) tillage treatments on characteristics of C source utilization microbial structure in both rhizosphere and non‐rhizosphere soils under double‐cropping were investigated by using metagenome sequencing technology. The experiment included four tillage treatments: conventional tillage with crop residue incorporation (return), rotary tillage with crop residue return, no‐tillage (zero‐tilllage) with crop residue return, and rotary tillage with crop residue removed as control. The results showed that relative abundance of Firmicutes, Alphaproteobacteria and Deltaproteobacteria in both rhizosphere and non‐rhizosphere soils was increased by combined application of tillage with crop residue return practice. Regarding the cluster of orthologous groups of proteins categories, the largest group was 'amino acid transport and metabolism' with 0.223% unigenes, followed by 'general function prediction only' (0.205%), and 'nuclear structure' (0.005%) was the smallest group. And the gene ontology categories with different tillage treatments in following decreasing order: biological process (144,229, 42.4%) > cellular component (104,981, 30.8%) > molecular function (91,284, 26.8%). The principal coordinate analysis indicated that different parts of root zone and tillage treatments were the most and the second most important factors affecting the variation of C source utilization bacteria community, respectively. Therefore, the results showed that combined application of tillage with crop residue return practice significantly increased the C source utilization of soil microorganisms in the double‐cropped rice fields.