Background: Owing to specific working environments, it is important to attain sustainable development goals for the health of fishery workers during climate change. Fishery workers have a hazardous working environment, leading to specific injuries and fatal events. However, limited studies have investigated the health status of fishery workers through long-term longitudinal follow-up and compared it with that of farmers and employed workers with similar socioeconomic status. Methods: The Longitudinal Health Insurance Database 2000, a subset of the Taiwan National Health Insurance Research Database was used for this retrospective cohort study. Only fishery workers, farmers, and employed workers were included. Based on the majority of causes of death and related diseases, participants newly diagnosed with 18 diseases, classified into cardiometabolic diseases, mental illness, chronic kidney disease, infection, and malignancy, were included. Participants with an old diagnosis of these diseases were excluded. All included participants were followed up from 1 July 2000 to the diagnosis and withdrawal date, or 31 December 2012, whichever occurred first. Due to the substantial difference in the baseline demographics, we executed a cohort study with propensity score-matched and applied the Cox model to explore the participants’ health status. Results: After matching, there were negligible differences in the baseline demographics of fishery workers, farmers, and employed workers. Compared to farmers and employed workers, fishery workers were more frequently diagnosed with 11 and 14 diseases, respectively, such as hypertension (hazard ratio [HR]: 1.11, p < 0.01), diabetes (HR: 1.21, p < 0.001), dyslipidemia (HR: 1.18, p < 0.001), depression (HR: 1.38, p < 0.001), peptic ulcer (HR: 1.17, p < 0.001), chronic viral hepatitis (HR: 2.06, p < 0.001), hepatocellular carcinoma (HR: 1.67, p < 0.001), and total malignancy (HR: 1.26, p < 0.001). Conclusions: Compared to farmers and employed workers, fishery workers were more impacted by cardiometabolic diseases, mental illness, infection, and malignancy. Therefore, it is imperative to specifically focus on health policies for fishery workers, such as providing curable antiviral treatment and initiating culture-tailored health promotion programs, to mitigate health inequality.