China has experienced urbanization at high speed and at an unprecedented scale. As a key support system for human survival and development, city is a typical case of coupled human and natural systems (CHANS). Harmonization of coupled human and natural systems in urban area is an important content of understanding the coupling mechanism between human and nature, which is of great significance to reveal the impact of human activities on ecological environment and plays a key role in guiding city construction. In this study, we created a comprehensive index system with water resource intensity, land development intensity, water supply capacity, effluent intensity and carbon emission intensity to estimate the impact of urban development on the natural environment. Based on calculation of the harmonization index for 146 major cities in China in 2016, we analyzed how population scale, economic level, social development level and eco-geographical regions would relate to harmonization of coupled human and natural systems. The results show that (1) in 2016 the national harmonization index was 87.90, but there was a large range in the level of harmonization across cities, with the best city was 98.83 and the worst was 14.39. (2) The degree of harmonization was negatively correlated with city population size, and the harmonization index order was the "small and medium size city" (89.11) > the "big city" (88.10) > the "mega-city" (87.26) > the "super city" (76.12). (3) Under different economic levels, harmonization was also negatively related to the economic level. The order of harmonization index was as follows, the "class IV city"(94.02) > the "class III city"(86.83) > the "class II city"(81.56) > the "class I city"(78.07). (4) The harmonization index had a significantly negative correlation with the level of urban social development. The higher per capita GDP, the lower harmonization index. (5) For the harmonization index values of the six eco-geographical regions, the Southwest received a score of 92.81 while the Northwest only was scored 82.25. It is found that the urban construction and development in China still have a huge impact on the natural environment, which is reflected in the following aspects:(1) the urban development in China is still in the development stage with high demand and caused high emission. (2) The carrying capacity of ecological environment plays an important role on affecting the cities' harmonization of coupled human and natural systems. (3) Improving efficiency of energy utilization and reducing intensity of the carbon emission will engage the acceleration of the harmonization of coupled human and natural systems in urban areas. Last but not least, we make some policy suggestions from the aspects of optimizing the urban layout, improving the efficiency of water and energy utilization, controlling environmental pollution, etc., which can provide reference and basis for evaluating the construction and sustainable development of urban ecological civilization.