In terms of aquiculture scale, the total oyster production of Taiwan in 2021 is about 18,000 metric tons, with an output value of about NTD 4 billion. It is one of the most important economic shellfish aquiculture industries in Taiwan. However, there are occasional reports of mass deaths of oysters as well as diseases and parasites by news media. In addition, foreign oyster imports have soared. Due to the double blow of domestic and foreign factors, Taiwan’s oyster aquiculture industry is encountering operational difficulties, and its total output and output value have shown a downward trend in recent years. In order to understand the challenges and problems of oyster farmers in major oyster aquiculture sites in Taiwan, we employed in-situ surveys and questionnaires to explore the challenges in different aquiculture sites and their degree of importance. According to the results, in addition to the degree of importance of industrial challenges considered by farmers in major oyster aquiculture sites in Taiwan, the most common challenges faced by farmers include (C1) the mass import of Vietnamese oysters (imported oysters), and (A1) the environmental degradation and (D5) lack of dredging in the oyster aquiculture sites. These factors have attributed to increased risks and decreased profits in oyster aquiculture, loss of areas suitable for oyster aquiculture, and decreased aquiculture output in many oyster farmers. At this stage, in addition to strengthening spot checks and inspections of imported oysters as well as mandating the provision of certificates of origin and labeling quality control, it is also necessary to improve the market segmentation for and quality of Taiwan oysters. A simple and direct investigation and analysis method that is closely aligned with industry standards has been proposed in this study to analyze the opinions and suggestions of farmers in different oyster aquiculture sites pertaining to the industrial challenges they face. The results provide a reference for government-industry-academia to understand the actual needs of each oyster aquiculture site, and devise solutions for each site through appropriate plans that are tailored to local conditions.