Aerosol samples were collected during pre-monsoon, monsoon and post-monsoon periods in 2009 in Lijiang, a tourism city located on the southeast Tibetan Plateau, southwest China. To determine the seasonal variation and sources of aerosol species, main elements and water soluble ions were analyzed. The results showed that crustal elements (Si, K, Ca, Ti and Fe) were the main elements with an enrichment whose enrichment factor (EF) value were lower than 10, with the large value (except Ca) occurring during the pre-monsoon period. The EF values of S, Cl, Zn, As, Br, Sb, Pb, and Cu were higher than those of the crustal elements and the large concentration appeared during the monsoon period. Ca2+ and SO42– were the dominant cation and anion, respectively. The greatest value of total ionic concentration was found during the monsoon period, mainly because of the high concentration of SO42– and NH4+. Using the positive matrix factorization model, it was found that the main sources of species were from crustal source, transport from south Asia and eastern China, local vehicle emissions and sea salt. Further results indicated that the pollutants mixed with dust, anthropogenic pollutants and biomass burning emissions can be transported to Lijiang from south Asia and Southeast Asia during the pre-monsoon period. In addition, pollutants rich in SO42– and heavy metal from the Sichuan Basin and eastern Yunnan Province can also be occasionally transported to Lijiang during the monsoon period. The seasonal differences in chemical composition and transportation pathway may have important implications for regional climate change.