The molecular mechanisms underlying the biological effects of carbon ions are unclear. The aim of this study was to explore the Wnt/β-catenin pathway in regulating carbon ion ( 12 C 6+ ) radiation-induced cellular toxicity. HLY78 is a Wnt-specific small molecular modulator, whose effects on 12 C 6+ radiation-induced damage are mostly unknown. HLY78, in combination with 12 C 6+ radiation was investigated on HeLa cell viability, cell cycle progression, DNA damage, and the expression of apoptotic and Wnt-related proteins. 12 C 6+ radiation suppressed cell viability in a time-dependent manner, whereas the addition of HLY78 to cells significantly reduced this stress. Moreover, after irradiation with 12 C 6+ , HeLa cells exhibited increased cell apoptosis, G2/M phase arrest, and a number of γ-H2AX foci. However, Wnt signaling activation alleviated these effects. Furthermore, when compared with the radiation alone group, supplementation with HLY78 markedly increased the expression of anti-apoptotic and Wnt-related proteins, and significantly decreased the expression of apoptotic proteins. The present results indicated that activation of the Wnt/β-catenin signaling pathway by HLY78 reduced 12 C 6+ radiation-induced HeLa cell dysfunction, suggesting that the Wnt/β-catenin signaling pathway plays an important role in regulating 12 C 6+ radiation-induced cellular toxicity in HeLa cells.