Timber harvesting is common disturbances of forest ecosystem and different harvest methods have different effects on forest ecosystem. The unreasonable harvest method will cause soil nutrient loss, reduce soil water holding capacity, and lead to serious consequences such as soil erosion and forest degradation. The Great Xingan Mountain forest ecosystem has the largest forest area and the largest forest stock in China. L. gmelinii is the main zonal vegetation in this area. Therefore, the restoration of L. gmelinii is of great importance to the Great Xingan Mountain forest ecosystem after harvesting. Clear cutting and shelter-wood cutting sites in 1987 and 2013 and uncut contrast site in the Great Xingan Mountain, Genghe, Inner Mongolia were selected as the research area. We sampled the rhizosphere soil of L. gmelinii in sites and analyzed its physicochemical properties and microbial community characteristics. The results showed that change of physical and chemical properties and characteristics of microbial community of rhizosphere soil after timber harvesting were different from that of non-rhizosphere soil, and the physical and chemical properties and microbial community of rhizosphere soil of L. gmelinii would be affected differently by different harvest methods in different stage of restoration. (1) Fungi in rhizosphere and non-rhizosphere soil microbial communities were both more susceptible to the effects of soil physical and chemical properties than bacteria, but the change of single physical and chemical properties could not significantly affect the rhizosphere and non-rhizosphere soil microbial communities. (2) Compared with the uncut contrast site, in the early stage of restoration of clear cutting, no significant changes were found in the physical and chemical properties, microbial community structure and diversity of the rhizosphere soil of L. gmelinii. In the late stage of restoration of clear cutting, the physical and chemical properties (total carbon, total nitrogen, available nitrogen and pH) of the rhizosphere soil of L. gmelinii changed significantly, resulting in a significant decrease in microbial biomass carbon and nitrogen, the content of phospholipid fatty acid (PLFA) of fungi, a significant increase in bacteria/fungi, and a significant decrease in Simpson diversity index. (3) For shelter-wood cutting sites, in the early stage of restoration, the contents of total carbon, total nitrogen, available nitrogen and water content in the rhizosphere of L. gmelinii were significantly reduced. The content of total potassium and available phosphorus were significantly increased, the microbial biomass was significantly lower than that of the contrast site. At the late stage of restoration, the ratio of carbon to nitrogen and the content of total phosphorus increased significantly, and the microbial biomass carbon returned to the level before shelter-wood cutting. Shelter-wood cutting had no significant effect on PLFA content, microbial community structure and diversity of all microbial groups in rhizosphere soil.