Wood sapstain is a serious problem caused by the wood stain fungus, and it has a great influence on the international wood industry. The utilization of biological methods has good prospects for wood conservation. The objective of this study was to systematically estimate the antagonistic effect and influencing factors of Bacillus subtilis against wood stain fungus by using meta-analysis of literature data. Through report retrieval, a total of 992 references on B. subtilis related to wood were obtained. After strict screening, 163 data items from 7 articles were integrated. Estimated by the random-effects model, the combined effect Odds Ratio of the overall antagonistic effect was 0.15 (95% confidence interval [0.06, 0.34]). The results showed that B. subtilis could produce significant antagonistic effects against wood stain fungi. The inhibitory effect of wood stain fungi was affected by the strains of B. subtilis, species of wood stain fungi, the B. subtilis dosage, the type of mixed reagent, and the amount of mixed reagent on different wood stain fungi. The results of this study may provide a reference for biological control experiments, field tests, and practical applications of wood conservation.