Based on daily climate data from national base climatological stations for the period of 1951—2009 and urban population data for the period of 1986—2008, a new urbanization index was established, climatic effect of urbanization in Beijing-Tianjin-Hebei region, the Yangtze River Delta region, the Pearl River Delta region and typical cities of three mega city agglomerations was analyzed, and the characteristics of urbanization effect among three regions were compared. The results indicate that daily mean and minimum temperatures increased remarkably under the influence of rapid urban progress. According to seasonal variation of urbanization effect, typical cities can be classified into three groups. In the first group, warming is most obvious in cold seasons; for the second group, the intensity of warming is the strongest in hot seasons; the last group experiences most evident warming in transition seasons. The overall effect on climate was strongest in the Yangtze River Delta, and weakest in the Pearl River Delta. In both Beijing-Tianjin-Hebei region and the Yangtze River Delta, daily mean and minimum temperatures were significantly increasing, with obvious warming in spring and autumn. The difference between two regions were in two aspects: urbanization effect was stronger in summer than in winter for the Yangtze River Delta, while its opposite for Beijing-Tianjin-Hebei region; warming rate of daily maximum temperature was positive in the Yangtze River Delta, but it was nearly zero in Beijing-Tianjin-Hebei region. Urbanization effect on precipitation varied among three regions, mainly influencing precipitation extremes.