The distribution of economic loss associated with vessel accidents typically exhibits non-negative, continuous, positively skewed, and heavy-tailed characteristics. Another challenge in analyzing fishing vessel accidents is the absence of relevant factors. Ignoring such heterogeneity caused by unobserved factors potentially leads to inaccurate inferences. In the present study, a novel Bayesian random-parameter generalized beta of the second kind (GB2) model with possible heterogeneity in means and variances was developed. The flexible GB2 distribution was harnessed to model the skewed and heavy-tailed response variable, while the random parameters were specified to capture the unobserved heterogeneity. The proposed method was validated using an insurance claim dataset with 3448 fishing vessel accidents within Ningbo waters during 2018–2022. The proposed model successfully identified significant influential factors, including fixed parameters, random parameters, and covariates influencing the means of the random parameters. Specifically, offshore and inevitable accidents, fishing transport vessels, double-trawl vessels with mechanical failures, wide-hulled vessels, and favorable sea conditions were associated with greater economic loss. Special attention should also be paid to nighttime accidents involving steel-hulled fishing transport vessels, as this accident type emerged to result in greater loss during the pandemic lockdown period. Our approach can accommodate the abnormality, skewness, and heavy-tail of vessel accident loss data, adjust for the bias introduced by unobserved factors, and uncover the interactive relationship among covariates. Targeted countermeasures were proposed to mitigate economic loss resulting from fishing vessel accidents.