Modeling the heat and carbon dioxide (CO2) exchanges in agroecosystems is critical for better understanding water and carbon cycling, improving crop production, and even mitigating climate change, in agricultural regions. While previous studies mainly focused on simulations of the energy and CO2 fluxes in agroecosystems on the North China Plain, their corrections, simulations and driving forces in East China are less understood. In this study, the dynamic variations of heat and CO2 fluxes were simulated by a standalone version of the Simple Biosphere 2 (SiB2) model and subsequently corrected using a Random Forest (RF) machine learning model, based on measurements from 1 January to 31 May 2015–17 in eastern China. Through validation with direct measurements, it was found that the SiB2 model overestimated the sensible heat flux (H) and latent heat flux (LE), but underestimated soil heat flux (G0) and CO2 flux (Fc). Thus, the RF model was used to correct the results modeled by SiB2. The RF model showed that disturbances in temperature, net radiation, the G0 output of SiB2, and the Fc output of SiB2 were the key driving factors modulating the H, LE, G0, and Fc. The RF model performed well and significantly reduced the biases for H, LE, G0, and Fc simulated by SiB2, with higher R2 values of 0.99, 0.87, 0.75, and 0.71, respectively. The SiB2 and RF models combine physical mechanisms and mathematical correction to enable simulations with both physical meaning and accuracy.