A flux-form semi-Lagrangian transport scheme (FFSL) was implemented in a spectral atmospheric GCM developed and used at IAP/LASG. Idealized numerical experiments show that the scheme is good at shape preserving with less dissipation and dispersion, in comparison with other conventional schemes. Importantly, FFSL can automatically maintain the positive definition of the transported tracers, which was an underlying problem in the previous spectral composite method (SCM). To comprehensively investigate the impact of FFSL on GCM results, we conducted sensitive experiments. Three main improvements resulted: first, rainfall simulation in both distribution and intensity was notably improved, which led to an improvement in precipitation frequency. Second, the dry bias in the lower troposphere was significantly reduced compared with SCM simulations. Third, according to the Taylor diagram, the FFSL scheme yields simulations that are superior to those using the SCM: a higher correlation between model output and observation data was achieved with the FFSL scheme, especially for humidity in lower troposphere. However, the moist bias in the middle and upper troposphere was more pronounced with the FFSL scheme. This bias led to an over-simulation of precipitable water in comparison with reanalysis data. Possible explanations, as well as solutions, are discussed herein.