Two new morpholine ionic liquid heteropolyacid salts were synthesized by a two-step proceeding. They were [C3SO3Hnhm]3PW12O40 and [Nbmm]3PW12O40. The structure of IL was characterized by FT-IR and 1H NMR spectra. The thermal stability was characterized by TG. At the same times, the solubility of ionic liquid heteropolyacid salt was also studied. In addition, the catalytic activity of [C3SO3Hnhm]3PW12O40 for the transesterification of soybean with methanol was investigated. The results show that under the optimized conditions of n(methanol):n(soybean)=14:1, catalyst dosage was 4%, reaction temperature was 100 oC and reaction time was 6 h, the yield of biodiesel up to 94.90%. The IL could reuse more than 6 times, and it will without a significant decrease in activity after regeneration by drying under vacuum. During the transesterification process, [C3SO3Hnhm]3PW12O40 was self separation catalyst induced by the reaction. The catalytic activity was increased and the catalyst was easy to be recycled and used repeatedly, which was due to [C3SO3Hnhm]3PW12O40 has the characteristic of homogeneous reaction in the high temperature and heterogeneous separation in the low temperature.