Shift work may adversely affect individuals’ health, thus, the current study aimed to investigate the association between shift work and health outcomes in the general population. A total of 41,061 participants were included in this online cross-sectional survey, among which 9612 (23.4%) individuals engaged in shift work and 31,449 (76.6%) individuals engaged in non-shift work. Multiple logistic regression analyses were conducted to explore the association between shift work and health outcomes (psychiatric disorders, mental health symptoms, and physical disorders). In addition, associations between the duration (≤1 year, 1–3 years, 3–5 years, 5–10 years, ≥10 years) and frequency of shift work (<1 or ≥1 night/week) and health outcomes were also explored. The results showed that compared to non-shift workers, shift workers had a higher likelihood of any psychiatric disorders (odds ratios [OR] = 1.80, 95% CI = 1.56–2.09, p < 0.001), mental health symptoms (OR = 1.76, 95% CI = 1.68–1.85, p < 0.001), and physical disorders (OR = 1.48, 95% CI = 1.39–1.57, p < 0.001). In addition, inverted U-shaped associations were observed between the duration of shift work and health outcomes. These results indicated that shift work was closely related to potential links with poor health outcomes. The findings highlighted the importance of paying attention to the health conditions of shift workers and the necessity of implementing comprehensive protective measures for shift workers to reduce the impact of shift work.