Forest thinning is a major forest management practice worldwide and may lead to profound alterations in the fluxes of soil greenhouse gases (GHGs). However, the global patterns and underlying mechanisms of soil GHG fluxes in response to forest thinning remain poorly understood. Here, we conducted a global meta-analysis of 106 studies to assess the effects of forest thinning on soil GHG fluxes and the underpinning mechanisms. The results showed that forest thinning significantly increased soil CO2 emission (mean lnRR: 0.07, 95% CI: 0.03–0.11), N2O emission (mean lnRR: 0.39, 95% CI: 0.16–0.61) and decreased CH4 uptake (mean Hedges’ d: 0.98, 95% CI: 0.32–1.64). Furthermore, the negative response of soil CH4 uptake was amplified by thinning intensity, and the positive response of soil N2O emission decreased with recovery time after thinning. The response of soil CO2 emission was mainly correlated with changes in fine root biomass and soil nitrogen content, and the response of soil CH4 uptake was related to the changes in soil moisture and litterfall. Moreover, the response of soil N2O emission was associated with changes in soil temperature and soil nitrate nitrogen content. Thinning also increased the total balance of the three greenhouse gas fluxes in combination, which decreased with recovery time. Our findings highlight that thinning significantly increases soil GHG emissions, which is crucial to understanding and predicting ecosystem-climate feedbacks in managed forests.