There are significant differences in the tropical cyclone (TC) activities between the year 2004 and 2006 over the western North Pacific, in that TC formations occurred over the central and eastern part of the western North Pacific during July and September 2004, but over the South China Sea and the western part of the western North Pacific during July and September 2006. In this paper, the impacts of large-scale atmospheric factors and tropical synoptic-scale perturbation on tropical cyclogenesis over the western North Pacific during July-September 2004 and those in 2006 are analyzed and compared by using Joint Typhoon Warning Center (JTWC) best track data, National Centers for Environmental Prediction -Department of Energy (NCEP-DOE) Atmospheric Model Intercomparison Project Phase-II (AMIP-II) reanalysis data, and National Oceanic and Atmospheric Administration (NOAA) outgoing longwave radiation (OLR) data. The results show that there is no remarkable difference between the average position of the monsoon trough in 2004 and that in 2006. However, the shapes of the monsoon trough are quite different. In 2004, the trough line is not noticeable but a cyclonic vortex is located over the central western North Pacific as the prominent feature. However, in 2006, the principle feature of the monsoon circulation is the distinct trough line, and horizontal wind shear is characterized by straight horizontal flow to the north and south of the trough line. Besides, an important reason for the distribution of TC events is the zonal differences of low-level relative vorticity, high-level divergence and vertical wind shear between 2004 and 2006. Moreover, the evolutions of synoptic-scale wave trains with a 3-8-day period over the western North Pacific during July to September in the years of 2004 and 2006 are analyzed and compared. The results show a close relationship between the tropical cyclogenesis and synoptic-scale wave trains in both 2004 and 2006. A stronger synoptic-scale wave train is located over the central and eastern part of the western North Pacific in 2004, and a weaker synoptic-scale wave train is located over the South China Sea and western part of the western North Pacific in 2006, which could be ascribed to the horizontal differences of the transient eddy kinetic energy tendency through the shear and confluence of the zonal mean flow. Therefore, the differences between the large-scale environment and synoptic-scale waves during July to September 2004 and those in 2006 led to different TC activities, in that TCs tended to form over the eastern area in 2004 and over the western area in 2006.