Eddy covariance measurements were conducted on fluxes of moisture, heat and CO<sub>2</sub> in a near-surface layer over a non-uniform crop surface in an agricultural ecosystem in the central plain of China from 10 June to 20 July 2002. During this period, the mean canopy height was about 0.50 m. The study site consisted of grass (10% of area), bean (15%), corn (15%) and rice (60%). Based on footprint analysis, we expected >90% of the measured flux (at a height of 4 m above ground surface) to occur within the nearest 600 m of upwind area. We examined interdiurnal variations in the components of the surface energy balance and in CO<sub>2</sub> flux. Results show that the pattern of energy partition had no obvious variation during the season. Daytime absorption of CO<sub>2</sub> flux by the crop canopy suddenly increased after thunderstorm events. We examined the energy budget closure and found it to be around 0.85. We compared energy partitioning for all rain-free days, and found energy imbalance was more significant for the 1~3 days after rainy events and energy components almost achieve balance for the other rain-free days. It indicated that the cold or warm rainwater infiltrating into soil made problems.