Scheduling the night-shift and morning-shift duties pairing plan (NMDPP) is a common process in Chinese metro crew management. Since metro crews work in a special working environment, sufficient rest is essential for them. NMDPP will affect the rest time of crews on metro lines with multiple depots and handover points. To improve the rest time of crews, this paper proposes a binary programming model to optimize the NMDPP. Moreover, a hybrid algorithm combining General Variable Neighbourhood Search (GVNS) with an Assignment Algorithm is designed to find high-quality solutions for this problem. Finally, computational experiments with both artificial data and reallife data are conducted. The results indicate that the GVNS can obtain highquality solutions efficiently for various NMDPPs. Besides, the proposed method can effectively increase the rest time of crews compared to the practical method used in metro companies.