Objective. CT-mesh hybrid phantoms (or 'hybrid(s)') made from integrated patient CT data and mesh-type reference computational phantoms (MRCPs) can be beneficial for patient-specific whole-body dose evaluation, but this benefit has yet to be evaluated for second cancer risk prediction. The purpose of this study is to compare the hybrid's ability to predict risk throughout the body with a patient-scaled MRCP against ground truth whole-body CTs (WBCTs). Approach. Head and neck active scanning proton treatment plans were created for and simulated on seven hybrids and the corresponding scaled MRCPs and WBCTs. Equivalent dose throughout the body was calculated and input into five second cancer risk models for both excess absolute and excess relative risk (EAR and ERR). The hybrid phantom was evaluated by comparing equivalent dose and risk predictions against the WBCT. Main results. The hybrid most frequently provides whole-body second cancer risk predictions which are closer to the ground truth when compared to a scaled MRCP alone. The performance of the hybrid relative to the scaled MRCP was consistent across ERR, EAR, and all risk models. For all in-field organs, where the hybrid shares the WBCT anatomy, the hybrid was better than or equal to the scaled MRCP for both equivalent dose and risk prediction. For out-of-field organs across all patients, the hybrid's equivalent dose prediction was superior than the scaled MRCP in 48% of all comparisons, equivalent for 34%, and inferior for 18%. For risk assessment in the same organs, the hybrid's prediction was superior than the scaled MRCP in 51.8% of all comparisons, equivalent in 28.6%, and inferior in 19.6%. Significance. Whole-body risk predictions from the CT-mesh hybrid have shown to be more accurate than those from a reference phantom alone. These hybrids could aid in risk-optimized treatment planning and individual risk assessment to minimize second cancer incidence.