The biodiesel was synthesized via transesterification from xanthoceras sorblfolia bunge seed oil and cottonseed oil produced in Xinjiang. Fatty acid methyl ester from biodiesel was analyzed by GC/MS technique. Their fuel properties were also tested and compared with the standards of diesel fuel and biodiesel produced in Europe and America. The influence of the structure and content of esters on fuel properties were analyzed. The results showed that xanthoceras sorblfolia bunge seed oil was better than cottonseed oil as resources.