In order to study the most efficient 2-DE protocol of Fokienia hodginsii proteomics, three different methods including TCA-acetone, phenol extraction method and TCA-phenol extraction method were tested in the experiment. Besides, three different IPG strips of pH3~10, pH5~8, pH4~7 combined with three different focusing parameter which showed 20 000, 25 000, 30 000 Vh respectively were performed in IEF. Finally, different concentration separation gel (10%,12.5%)were performed in all SDS-PAGE trial. The results indicated that more protein spots were detected on 2-DE gels by phenol extraction method, IPG strips of pH4~7, 25 000 Vh focusing parameter, and 10% separate gel were the best settings of the 2-DE protocol. The experiment preliminary established the 2-DE protocols of F. hodginsii leaves which would be beneficial for the further study of proteinmics.