Guanidinylated chitosan (GCS), as a heterogeneous alkaline catalyst for the transesterification of soybean oil with methanol, was synthesized by grafting aminoiminomethanesulfonic acid onto chitosan. The structure and properties of GCS membrane were investigated by Fourier transform infrared spectroscopy, thermogravimetry and X-ray photoelectron spectroscopy. The soybean oil conversion reached 98.8% at the first run and 96.6% at the fifth run under the reaction conditions: catalyst amount of 20wt.%, methanol/oil mass ratio of 2.5:1 at 60°C for 6h. Results show that the transesterification mainly took place on the surface of the catalytic membrane. The kinetics study of the transesterification was undertaken in terms of pseudo-homogeneous model and performed as a first order reaction with an activation energy of 76.95kJ/mol and pre-exponential factor of 7.94×109min−1.