In this study, the liquid lipase Yarrowia lipolytica lipase 2 (YLLip2) expressed by Pichia pastoris GS115 was used to produce biodiesel from waste oil. Four signal peptides were compared to express YLLip2 in P. pastoris, among which SP23 exhibited greater secretion performance. In a 1.3-L bioreactor with FM22 medium for 7 d incubation, the maximum YLLip2 activity and 30 total protein content reached 895.44 ± 27.31 U/mL and 3.83 ± 0.31 g/L, respectively. Under the optimal reaction conditions of 30 ℃, 20% moisture content, 50 U/g oil of enzyme dosage, and distributed methanol addition, the reaction yield reached 80.99% after 12 h. In the presence of additives such as glucose or β-cyclodextrin, the yield was slightly improved. To further improve the biodiesel yield, lipase GS “Amano” 50 (G50) was used to synergize with YLLip2. The results showed that adding G50 (approximately 1/20 of YLLip2) increased the yield by approximately 90% after 6 h cultivation without changing the enzyme dosage. Compared with previous studies, the reaction time for biodiesel production from waste oil in this study was significantly shortened. This study provides a workable method for converting low-quality feedstocks containing high-free fatty acids into biodiesel using a liquid lipase as the catalyst.