Abstract: For the purpose of study on the characteristics of the boundary layer and its effects on air pollution in the Pearl River Delta, the comparison observation based on balloon sounding is conducted by Sun Yat-Sen University in Qingyuan, Panyu and Xinken of the Pearl River Delta in October, 2004. The temperature and wind profiles of the boundary layer over the Pearl River Delta in autumn are studied on the observation data.It is found that the temperature lapse rate is small while the occurrence frequency of the temperature inversion is high and the intensity is low over the Pearl River Delta in October, 2004. The surface temperature inversion occurs earlier over the city cluster than over the Pearl River estuary and the average intensity over the city cluster doubles that over the Pearl River estuary while the low-lever temperature inversion frequency over the city cluster is lower than that over the Pearl River estuary. The relatively low temperature and the high-speed sea breeze postpone the occurrence time of the surface temperature inversion and increase the occurrence frequency of the low-lever temperature inversion over the Pearl River estuary.It is also found that the Pearl River Delta is influenced by several kinds of local circulations and the wind profiles of the boundary layer are complex in October, 2004. The prevailing wind direction is northeast, and in the daytime the wind directions of the three sites are consistently in the northeast while in the nighttime there are obvious differences in wind direction between the city cluster and the non-city cluster, which is that the wind direction of the non-city cluster (Qinyuan and Xinken) is in the northeast and that of the city cluster is in the northwest. The city cluster is markedly characterized by local circulations and heat island circulation is frequently observed at night; the Pearl River estuary is markedly characterized by gradient wind and sea breeze circulation is frequently observed at night, and the occurrence frequency of 20-hour sea breeze is 51.8%; the local circulations of both the city cluster and the Pearl River estuary are observed under the same meteorological background of low-speed system wind and basically on the same dates.