Understanding the impact of meteorology on the vertical variation of PM2.5 is of importance to clarify the formation of the haze. This study conducted an investigation of PM2.5 and synchronous meteorological variations in a three-dimensional space by a lightweight unmanned aerial vehicle (UAV) equipped with portable monitors. The field campaign was carried out for five days from August, 2014 to February, 2015, within 1000 m altitude of a 4 km *4 km area in Lin’an, China. The UAV measurement was done four times every day and each flight was flied along a designed spiral route from ground up to 1000 m altitude. PM2.5 mass concentration and meteorological factors including air temperature, relative humidity, dew point temperature and air pressure were sampled at three-dimensional spatial locations during each flight. Five days’ measurements show that PM2.5 horizontal distribution is more homogenous than its vertical distribution. PM2.5 level decreases with the increase of height, and has more obvious stratification in morning flights but more homogeneity in afternoon flights within 1000 m lower atmosphere. PM2.5 value above 500 m altitude is a little higher in the afternoon especially for more stratification days. The vertical gradient of PM2.5 concentration decreases from morning to afternoon, which is weaker in winter than in summer and autumn. The coupling role of meteorological factors results in the change of planetary boundary layer height and inversion layer, which further exerts a significant impact on PM2.5 change within the lower troposphere. These results provide a helpful reference in analyzing and forecasting PM2.5 pollution in future.