Rice panicle temperature (Tp) is a key factor for studying high temperature impacts on spikelet sterility. Comparing with measuring Tp by hand, a Tp simulation model could obtain Tp data readily. The two-layer energy budget model which divides the soil layer and canopy layer was widely used to predict rice canopy temperature (Tc), but panicle existed mostly in the upper layer canopy, and we have proved that Tc was different from the upper layer canopy temperature (Tc1), and the upper layer must be separated from the whole canopy for the purpose of estimating Tp. Thus, we developed the three-layer model, contained upper canopy layer with panicle (50–100 cm), lower rice canopy layer (10–40 cm), and water surface layer (≤10 cm) to estimate Tp with general meteorological and vegetation growth data. There were two steps to estimate Tp. The first step was calculating Tc1 and lower layer canopy temperature (Tc2) by solving heat balance equations with canopy resistances. And the second step was estimating Tp with following parameters: (a) the inclination factors of leaves and panicles (F1, F2, and Fp) which were decided by fitting the calculated transmissivity of downward solar radiation (TDSR) to the measured TDSR, (b) the aerodynamic resistance between the panicle and atmosphere (rap) denoted by wind speed, (c) the panicle resistance for transpiration (rp) denoted by days after heading, and (d) air temperature and humidity at the panicle’s height (Tac1 and eac1) calculated from the resistances of the pathways of sensible and latent heat fluxes in accordance with Ohm’s law. The model simulated fairly well the Tc1, Tc2, and Tp with root mean square errors (RMSEs) of 0.76°C, 0.75°C, and 0.81°C, respectively, where RMSE of measured Tp and predicted Tp by integrated micrometeorology model for panicle and canopy temperature (IM2PACT) including two-layer model was 1.27°C. This model was validated well by two other rice cultivars, and thus, it demonstrated the three-layer model was a new feasible way to estimate Tp.