This study first collects the current status of overtime labor and well-being among young employees through literature research, based on which three research hypotheses are proposed. Secondly, in terms of empirical research, relying on the database of the Chinese Labor-force Dynamics Survey (CLDS) in 2018, this paper constructs a linear regression model and a moderation effect model to investigate the impact of overtime labor on the well-being of young employees and the moderating role of job autonomy between the two. Finally, the research findings indicate that: firstly, overtime labor has a negative effect on the well-being of young employees; secondly, there is a significant positive relationship between job autonomy and well-being; thirdly, job autonomy mitigates the negative impact of overtime labor on the well-being of young employees. Therefore, this study aims to provide relevant policy suggestions from multiple aspects to enhance the well-being of workers, reduce the adverse effects of overtime labor on young employees, safeguard their legitimate rights and interests, improve their working environment and quality of life, and ultimately achieve mutual benefit and win-win results for both employers and employees.