Abstract: Rice and wheat are two primary food crops, while rice-wheat rotation is one of the largest crop rotational systems with planting area of 24-26 million hm2 in the world. In China, the planting area accounts for about 34%-50% of the world’s total planting area, mainly distribute in Jiangsu, Zhejiang, Hubei, Sichuan, Anhui, Guigzhou and Yunnan Province. The studies on water and heat flux over rice-wheat rotation field continue to draw research attention. The research on the characteristic of water and heat flux and influencing factors over rice-wheat rotation field can provide basic information for field irrigation management and crop water use efficiency. In this study, the water and heat fluxes over rice-wheat rotation were determined by a Bowen ratio energy balance system at Agro-Meteorology Research Station, Nanjing University of Information Science and Technology, located in Nanjing City, Jiangsu Province in China (32.21° N, 118.68° E, altitude 14.4 m). The purpose of the research is to explore the characteristic of water and heat flux and influencing factors over these two different fields based on these data and path analysis method. Results showed that the diurnal variations of water and heat fluxes over rice-wheat rotation field were single-peak curves. The average peak values of latent heat flux over rice field at noon were higher than those over winter wheat field. The energy was mainly consumed by latent heat flux. The ratio between latent heat flux and availably energy was 71% over winter wheat field, while was 106% and 122%, respectively for 2016 and 2017 seasons over rice field during the whole growth stage. This result indicated that the rice canopy absorbed sensible heat flux for water consumption. The latent heat flux over rice field was higher than the availably energy during 66% and 81% of the growth season for two seasons, respectively. The daily average surface soil heat fluxes over rice-wheat rotation and water surface heat fluxes over rice field can be neglected due to the small differences. The value of Bowen ratio was positive for wheat, while negative for rice. The order of correlation coefficient between latent heat flux over rice and wheat rotation field and influencing factor was net radiation > vapour pressure deficit > air temperature at 1.5 m height above ground > wind speed. The direct path coefficient followed the same order. The effect of net radiation on latent heat flux over rice-wheat rotation field was primarily on direct effect. While the effect of air temperature at 1.5 m height, vapour pressure deficit and wind speed on latent heat flux was mainly on indirect effect through the interaction between them and net radiation. Decision coefficient results showed that the net radiation was the dominate environment factors affected latent heat flux at short time, followed by vapour pressure deficit. The decision coefficient was negative between air temperature at 1.5 m height above ground and latent heat flux, indicating that high air temperature in summer during rice growth period or low air temperature in winter during wheat growth period inhibited latent heat flux over rice or wheat field. The direct effect of net radiation on latent heat flux over rice field was higher, while vapour pressure deficit was lower than that over winter wheat field. The indirect effect of these factors on latent heat flux over rice field was higher than that over winter wheat field.