An approach based on the hidden Markov model (HMM) is proposed for risk performance reasoning (RPR) for the bauxite shipping process by Handy carriers. The unobservable (hidden) state process in the approach aims to model the underlying risk performance, while the observation process was formed from the time series of risk factors. Within the framework, the log-likelihood probability was used as the measure of similarity between historical and current data of risk reasoning factors. Based on scalar quantization regulation and risk performance quantization regulation, the RPR approach with different step sizes was conducted on the operational case, the performance of which was evaluated in terms of effectiveness and accuracy. The reasoning performance of the HMM was tested during the validation period using three simulated scenarios and one accident scenario. The results showed significant improvement in the reasoning capacity, and satisfactory performance for numerical risk reasoning and categorical performance reasoning. The proposed model is able to provide a reference for risk performance monitoring and threat pre-warning during the bauxite shipping process.