The possible impact of increasing global temperatures and altering oceanic conditions on the distribution of marine organisms raises significant concerns about the effects of climate change on marine ecosystems. The flathead gray mullet ( Mugil Cephalus L.) is a cosmopolitan fish that lives in the warm and temperate zones over 42°N–42°S. It is a key fish species for industrial fishing off coastal Taiwan. Gray mullets enter the coastal waters of the southeastern Taiwan Strait (22°N–25°N) to spawn in winter and feed in the coastal and tidal waters of China (25°N–30°N). From 1986 to 2010, the annual catch of grey mullet decreased substantially and remained low. Although the Pacific Decadal Oscillation and El Niño–Southern Oscillation are recognized to affect gray mullet migration, the increase in sea surface temperature may be the main cause of the aforementioned decrease. We explored how weather changes affect fishing conditions and patterns at the gray mullet fishing grounds in Taiwan’s coastal areas. Because of the decrease in gray mullet catches, the most common method for catching gray mullet in Taiwan’s coastal areas between 1990 and 2010 was the use of drift or trawl nets instead of two-boat purse-seiner fleets. Since 2012, purse-seiner fleets have become the most common method for catching gray mullet. This trend indicates that the local fishing industry is adapting to changing environmental conditions. The grey mullet populations in the Taiwan Strait have experienced a complete collapse. Therefore, it is imperative for fisheries management organisations to adopt ecosystem-based management strategies in order to ensure the maintenance of biologically viable levels of species stock. By integrating current knowledge into managerial plans, decision-makers may make informed decisions that will also protect the other fisheries of the Taiwan Strait and the people who rely on them amid changing climatic conditions.