Large divergence of the post-thinning change in soil carbon contents has impaired the evaluation of the thinning effect on forest carbon storage reported in previous case studies. In this context, the present study used a multi-site approach to assess the effect of thinning on forest floor and mineral soil carbon contents. The sites included four pine (Pinus densiflora Sieb. et Zucc.), five oak (Quercus spp.), and four larch (Larix kaempferi (Lamb.) Carr.) forests under the temperate climate, each of which included un-thinned control, intermediate thinning (15–30% basal area reduction), and heavy thinning (30–50% basal area reduction) treatments. Forest floor and mineral soil (0–10, 10–20, and 20–30 cm depths) carbon contents were determined 0–1, 3–4, and 6–7 years after thinning. The average forest floor and mineral soil (0–30 cm) carbon contents (Mg C ha−1) were 6.7 and 54.1 under the control, 6.6 and 60.7 under the intermediate thinning treatment, and 6.0 and 64.7 under the heavy thinning treatment, respectively. There was a slight decrease in forest floor carbon contents but an increase in mineral soil carbon contents under the thinning treatments, although the magnitude and direction of the thinning effect were site-specific. The magnitude of the thinning effects was stronger under the heavy thinning treatment than under the intermediate thinning treatment. However, the effect of thinning was unrelated to time after thinning and forest type. Topography (altitude and slope), soil properties (soil water content, pH, and total nitrogen concentration), diameter at breast height and height of remaining trees, and the percentage of removed basal area explained approximately 45% of variance in the thinning effect, indicating that differences in the environment are important in the divergence of the thinning effect on soil carbon contents across multiple sites. Our results suggest that designing thinning practices to foster forest carbon sequestration should consider the contribution of thinning intensity and environmental conditions to variation in the thinning effect on soil carbon contents.