To monitor growth and predict the yield of rice over a large area, the chlorophyll contents in the rice canopy were estimated using the unmanned aerial vehicle (UAV) remote sensing technology. In this work, multi-spectral image information of the rice crop was obtained using a 6-channel multi-spectral camera mounted on a fixed wing UAV, which was flown 600 m above the ground, between 11: 00-14: 00 on a sunny day in summer. The measured chlorophyll values were collected as sample sets. The s-REP index was screened out to estimate chlorophyll contents through the analysis of six kinds of spectral indexes of chlorophyll estimated capacity. An inversion model of the chlorophyll contents was then built using the least square support vector regression (LS-SVR) algorithm, with calibration and prediction R-square values of 0.89 and 0.83, respectively. Finally, remote sensing mapping for a UAV image of the Fangzheng County Dexter Rice Planting Park was accomplished using the inversion model. The inversion and measured values were then compared using regression fitting. R-square and root-mean-square error of the fitting model were 0.79 and 2.39, respectively. The results demonstrated that accurate estimation of rice-canopy chlorophyll contents was feasible using the LS-SVR inversion model developed using the s-REP vegetation index.