Biodiesel produced from non-edible oils has received intensive attention in recent years. Herein, a series of novel amphipathic ionic liquids (ILs) based on the 4-dimethylaminopyridine (DMAP) were prepared for the transesterification of soapberry oil and methanol. The structures of the prepared ILs were systematically characterized by both Fourier transform infrared spectroscopy (FT-IR) and nuclear magnetic resonance (NMR, H-1 NMR and C-13 NMR). In addition, the effects of side-chain length of cation and the number of active site (H+) of ILs on the biodiesel yield were investigated, and the results suggested that 1-dodecyl-(4-dimethylammonium)-pyridinium bisulfate ([C12-DMAPH][HSO4](2)) exhibited the highest catalytic efficiency. Meanwhile, [C12-DMAPH][HSO4](2) was proven to be amphipathic, and the corresponding catalytic mechanism was proposed. Under the catalysis of [C12-DMAPH][HSO4](2), the optimum operating conditions of transesterification of soapberry oil and methanol were explored via the combination of single factor experiment and response surface methodology, obtaining the high biodiesel yield of (98.02 +/- 0.36)% under the optimum operating conditions. Importantly, [C12-DMAPH][HSO4](2) exhibited high stability in the transesterification of soapberry oil and methanol in five consecutive runs. Furthermore, the catalytic activities of [C12-DMAPH][HSO4](2) towards other transesterification of non edible oils and lower alcohols were also investigated, which indicated a general applicability of the prepared IL. (c) 2020 Elsevier Ltd. All rights reserved.