This study explored the effects of long working hours (LW) and night work (NW) on subjective well-being and the modifying effects of work creativity and task variety (WCTV) and occupation. In addition, we examined the influence of working time-related variables including working-time mismatch, variability, shift work, and autonomy on the effects of LW and NW. This study used data from the 5th Korean Working Conditions Survey on 50,205 workers. LW and NW were defined as 52–60 h (L1) or >60 h (L2) per week, and 1–10 days (N1) or >10 days (N2) of night work per month. Multiple logistic regression was used to examine the effects of LW and NW and the modifying influences of WCTV and occupation. Differences in ORs of LW and NW caused by working time-related variables were investigated, to determine effect sizes and directions. A high level of WCTV alleviated the risks of LW and NW. White-collar workers were more vulnerable to the risk associated with NW. Regarding working-time related variables, working-time mismatch and variability increased the risks of LW and NW, respectively, while shift work alleviated the risks of NW. In countries where flexible work systems are not well utilized, working-time autonomy might not be associated with the risk of LW or NW. This study showed that it is necessary to comprehensively consider the occupation and task characteristics of individual workers performing LW or NW. Further studies of the modifying effects of working time-related variables on LW and NW are needed.