Background In the manufacturing industry, work-family conflict (WFC) is related to working hour characteristics. Earlier studies on the relationship between working hour characteristics and WFC in the manufacturing industry have been limited to some regions in Korea. No study has addressed the data on a national scale. Thus, this study investigated the impact of weekly working hours, weekend work, and shift work on WFC using national-scale data. Methods This study was based on the fifth Korean Working Conditions Survey of 5,432 manufacturers. WFC consists of 5 variables; WFC1 “kept worrying about work”; WFC2 “felt too tired after work”; WFC3 “work prevented time for family”; WFC4 “difficult to concentrate on work”; WFC5 “family responsibilities prevented time for work”. As WFC refers to the inter-role conflict between the need for paid work and family work, WFC has been measured in two directions, work to family conflict (WTFC: WFC1, 2, 3) and family to work conflict (FTWC: WFC4, 5). With these WFC variables, we conducted multiple logistic analyses to study how working hours, weekend work, and shift work impact WFC. Results Korean manufacturers’ prolonged working hours increased all aspects of WFCs. Odds ratios (ORs) of WFCs based on working hours (reference of under 40 hours) of 41–52, 53–60, over 61 were 1.247, 1.611, 2.279 (WFC1); 1.111, 2.561, 6.442 (WFC2); 1.219, 3.495, 8.327 (WFC3); 1.076, 2.019, 2.656 (WFC4); and 1.166, 1.592, 1.946 (WFC5), respectively. Shift-work in the WFC2 model showed a significantly higher OR of 1.390. Weekend work ‘only on Saturday’ had significant ORs with WFC2 (1.323) and WFC3 (1.552). Conclusions An increase in working hours leads to the spending of less time attending to problems between work and family, causing both WTFC and FTWC to increase. As weekends, evenings, and nighttime are considered to be family-friendly to people, working on weekends and shift-work were highly correlated to WTFC.