Stock assessment involves providing scientific and quantitative evaluations to objectively inform fisheries management. However, data limitations are a common challenge for global stock assessments. Many exploited fish stocks in China lack quantitative assessments due to the limitations imposed by the data requirements of conventional stock assessment methods; ultimately, this hinders the advancement of total allowable catch (TAC) systems in China. The catch-based maximum sustainable yield (CMSY) and Bayesian Schaefer production model (BSM) are recently developed methods that are most suited for calculating the intrinsic population growth rate (r), carrying capacity or unexploited stock size (k), maximum sustainable yield (MSY), and other reference points of data for fishery management. Reference points for 19 commercial groups exploited by Chinese fisheries were calculated over time using CMSY and BSM methods by evaluating catch and abundance levels. The results showed that one stock collapsed, three stocks were severely declined, five stocks were overfished, five stocks were slightly overfished, and five stocks were healthy. The long-term assessment of stock status demonstrated that the proportion of stocks at biologically sustainable levels declined from 95% in 1980 to 26% in 2019. We also compared the CMSY and BSM methods. The BSM method, which integrated CPUE data, resulted in wider confidence intervals and moderated the trend of biomass trajectories, with a final exploited biomass relative to the biomass at maximum sustainable yield (B₂₀₁₉/B_msy) for three stocks that exceeded the overfished threshold. This suggested that CMSY may overestimate or underestimate B/B_msy depending on the trend of stock abundance. Overall, independent fishery surveys should be conducted to obtain CPUE and biological data to improve assessment accuracy.