Numerous studies claim that rewetting interventions reduce CO2 and increase CH4 fluxes. To verify the claim, we conducted a systematic review and meta-analysis of the effects of rewetting on CO2 and CH4 fluxes and dissolved organic carbon (DOC). We identified 28 primary articles eligible for meta-analysis, from which we calculated 48 effect sizes for CO2 emissions, 67 effect sizes for CH4 emissions, and 5 effect sizes for DOC. We found that rewetting significantly decreased CO2 fluxes, with temperate zones showing the highest Hedges’ g effect size (−0.798 ± 0.229), followed by tropical (−0.338 ± 0.269) and boreal (−0.209 ± 0.372) zones. Meanwhile, rewetting increased CH4 fluxes, with the highest Hedges’ g effect size shown in temperate zones (1.108 ± 0.144), followed by boreal (0.805 ± 0.183) and tropical (0.096 ± 0.284) zones. In addition, based on yearly monitoring after rewetting, the CH4 emissions effect size increased significantly over the first 4 years (r2 = 0.853). Overall, the rewetting intervention reduced CO2 emissions by −1.43 ± 0.35 Mg CO2–C ha−1 year−1, increased CH4 emissions by 0.033 ± 0.003 Mg CH4–C ha−1 year−1, and had no significant impact on DOC. To improve the precision and reduce the bias of rewetting effect size quantification, it is recommended to conduct more experimental studies with extended monitoring periods using larger sample sizes and apply the before-after control-impact study design, especially in boreal and tropical climate zones.