Objective To investigate whether the reversal effect of rat bone marrow mesenchymal stem cells (BMSCs) on microglia in inflammatory response to ischemic stroke is mediated by ligand 1 of CX3C (CX3CL1). Methods A total of 30 rats were subjected in this study, and one rat was randomly selected for cerebral TTC staining. Modified Zea-Longa suture method was applied to establish rat model of middle cerebral artery occlusions (MCAO), and finally 20 model rats was recruited for the following experiments, including 2 rats undergoing TTC staining to detect cerebral infarction. The MCAO rats were randomly divided into control group (lateral ventricle localization injection of BMSCs, n=9) and experimental group (same injection of BMSCs after CX3CL1 lentivirus infection, n=9). The rats of 2 groups were decapitated on days 1,3 and 7 respectively to collect brain tissue. All brain tissue sections were subjected to anti-Iba and anti-CD206/TNF-α double immunofluorescence staining, and then the number of double positive cells was counted and compared under laser scanning confocal microscope. SPSS statistics 18.0 was used for statistical analysis. Data comparison between 2 groups was performed using Chi-square test. Results Rat MCAO model was successfully established, with infarcted lesions in the blood supply area of middle cerebral artery by TTC staining. The statistical results of immunofluorescence staining showed that compared with experimental groups, the number of anti-inflammatory microglia (Iba⁺CD206⁺) in the control group was significantly increased on days 1,3 and 7 [(8.644±1.131) vs (3.000±1.206), (7.866±1.254) vs (3.155±1.205), (7.111±1.555) vs (2.866±1.272) n/per 400×high-power field, all P<0.001], and the number of pro-inflammatory microglia (Iba⁺TNF-α⁺) was obviously decreased on days 3 and 7 [(4.222±0.974) vs (8.355±1.264), (4.267±1.321) vs (7.822±1.556) n/per 400×high-power field, both P<0.001]. Conclusion CX3CL1 may be the molecule mediating the reversal effect of BMSCs transplantation on microglia in cerebral ischemic area of MCAO rats.