The latest measurements from the two encounters of the MESSENGER spacecraft in year 2008 have discovered several interesting features of the magnetosphere of Mercury. We have performed high-resolution 3D hybrid model calculations to simulate the solar wind interaction with the Hermean magnetosphere during the first two Mercury encounters of the MESSENGER spacecraft in 2008. It is found that the global structure of the Hermean magnetosphere is significantly controlled by the direction of the interplanetary magnetic field. The bow shock size and shape and the magnetotail configuration have very large differences in these two encounters with northward-pointing and southward-pointing interplanetary magnetic field, respectively. Comparisons are also given with the observed magnetic field profiles and the computational results. In general, good agreement can be found including the interesting feature of the relatively thick magnetopause current layer at outbound measurements. Our work shows that 3D hybrid simulation is a promising method to study in detail the Hermean magnetosphere in parallel with the post-MOI observations of the MESSENGER spacecraft and the Bepi-Colombo mission in future.