Globally, marine fisheries have declined under multiple stresses including overfishing, climate change, and habitat degradation. The Min River Estuary, as the largest estuary in southeastern China, has confronted this situation over recent decades. In this study, the dominant species of fish stocks in the Min River Estuary, including Coilia mystus, Cynoglossus abbreviates, Collichthys lucidus, Amblychaeturichthys hexanema, Polydactylus sextarius, Harpodon nehereus, and Secutor ruconius, were evaluated by the length-based Bayesian biomass estimator method (LBB). Outcomes could be grouped into three categories as healthy, showing the lowest exploitation rate (E: 0.31–0.43) and highest relative biomass (B/B_msy: 1.30–1.90), including S. ruconius, C. mystus, and H. nehereus; overfished, with a medium E (0.50–0.58) and B/B_msy (0.68–0.79), including A. hexanema and C. abbreviates; and collapsed, with the highest E (0.89–0.92) and lowest B/B_msy (0.03–0.21), including C. lucidus and P.sextarius. Corresponding imperative countermeasures such as using larger-sized mesh gears and reducing fishing intensity should be deployed according to the current status of each species for sustainable fishery exploitation and fish conservation.