Microglia is one of the important non-neoplastic elements of cerebral glioma. The interaction of glioma and microglia promotes tumor progression. However, the spatiotemporal heterogeneity of the microglia in the context of glioma remains uncertain. In this study, cerebral glioma model was built with C6 cell implantation in 28 SD rats to investigate the distribution of microglia during the tumor progression. T2 weighted magnetic resonance imaging (T2WI) was conducted at the post-operative day 7, 9, 12, 14, 16, 18, 22, 23 and 24 after the model built-up, after which the Hematoxylin-Eosin (HE) and immunofluorescent staining of the brain tissue were prepared. Nine regions of interest (ROI) were defined within the tumor, as the peritumoral and the contralesional areas on the HE sections with the largest tumor expansion. Scale-invariant feature transform (SIFT) algorithm was used to register and fuse the HE-immunofluorescent image pairs. ROIs defined on the HE sections were then translated to the immunofluorescence images. The averaged signal intensity was measured on the T2WI image with the largest tumor diameter. Mean density (MD) of the microglia in the ROIs were measured for each ROI and plotted with the time after C6 cell implantation. It can be observed that MD in the tumor ROI was significantly larger than that of the rest ROIs (P＜0.001). MD increased with time and diameter that best fit to binomial and linear functions, respectively, for all the ROIs with a more precipitous inclination in the tumor MD. The average signal intensity of the ROIs on T2WI were also found positively correlated with the tumor MD. These findings indicate that tumor formation of C6 glioma triggers extensive microglia activation in the tumor and the non-neoplastic brain tissue, necessitating the assessment of microglia in both the local and global scales in performing the aggressiveness characterization and treatment trials targeting microenvironment of cerebral glioma.