The atmospheric boundary layer (ABL) is also known as the planetary boundary layer (PBL) which is directly influenced by its contact with the planetary surface. Surface heat fluxes usually include the sensible heat flux (SHF) and the latent heat flux (LHF), which have a great influence on the PBL. With the reanalysis data sets of planetary boundary layer height from NECP-FNL and the surface heat fluxes data from NCEP /DOE (NECP2), the temporal,spatial distribution and the variation trend of the planetary boundary layer height (PBLH), the sensible heat flux (SHF) and the latent heat flux (LHF) over the Qinghai-Tibetan Plateau have been studied with regional average. The mutation test was carried out by sliding T-test. The influence factors of boundary layer height and surface energy transport in plateau region were determined by correlation analysis and correlation coefficient test. The research time is the summer (June-August) from 2000 to 2016. The results showed that the HPBL of the whole Plateau during 2000-2016 is on the decline,the SHTFL is on the rise. The LHTFL from 2000 to 2009 is increase,but from 2009 to 2016 is decrease. The year of 2009 is the climate change time point of HPBL,at the same time the trend of other physical quantities also changed in 2009. The variation trend distributions have obvious regional differences. By the 91°E line,the plateau can be divided into two parts as the eastern and the western regions. The temporal,spatial characteristics from each part are obvious difference, and the year of 2009 is an abrupt change point of climate,also is a turning point of the annual variation tendency. The distribution of the temporal trend about the latent heat flux in the eastern and western regions is basically on the contrary between the period before and after the mutation. The impact factors of the eastern and the western region over the Qinghai-Tibetan Plateau are multiple,the main factor influenced the HPBL,SHTFL and LHTFL in the western region are the soil moisture from surface to 10 cm and the wind speed of 10 m,in contrast, the most important reason affects in the eastern region is the total cloud cover. Before and after the mutation-2009,the influence factors have big difference,for example the wind speed of 10 m has become the influence factor of surface latent heat flux in the eastern region after the abrupt climate change. The Heat Low develop in the plateau at surface layer over land and the South Asian High in the upper atmosphere,which provide the dynamic conditions for the development of the atmospheric boundary layer,it's good for the ascent. The air flow in the ascending motion can transfer the condensation latent heat released by the water vapor phase to the upper troposphere,which is beneficial to the positive feedback of latent heat flux and South Asian High.