Background: Integrating computational thinking (CT) into STEM education has recently drawn significant attention, strengthened by the premise that CT and STEM are mutually reinforcing. Previous CT-STEM studies have examined theoretical interpretations, instructional strategies, and assessment targets. However, few have endeavored to delineate the transfer effects of CT-STEM on the development of cognitive and noncognitive benefits. Given this research gap, we conducted a systematic literature review and meta-analysis to provide deeper insights. Results: We analyzed results from 37 studies involving 7,832 students with 96 effect sizes. Our key findings include: (i) identification of 36 benefits; (ii) a moderate overall transfer effect, with moderate effects also observed for both near and far transfers; (iii) a stronger effect on cognitive benefits compared to noncognitive benefits, regardless of the transfer type; (iv) significant moderation by educational level, sample size, instructional strategies, and intervention duration on overall and near-transfer effects, with only educational level and sample size being significant moderators for far-transfer effects. Conclusions: This study analyzes the cognitive and noncognitive benefits arising from CT-STEM’s transfer effects, providing new insights to foster more effective STEM classroom teaching.