The Fourier transform mid-infrared (FT-MIR) spectra and nitrogen concentration were measured from dried leaves of rice in booting stage under various treatments of nitrogen fertilization. The synergy interval partial least square algorithm (si-PLS) combined with genetic algorithm (GA) was applied to the selection of optimal variables. 84 variables were determined to build the estimation model for leaf nitrogen content. The prediction accuracy of the PLS regression model based on these variables was better than that of the siPLS model or the model from spectral index NFSA. The RMSEP (root mean square error of prediction) is 0.1186 and r (correlation coefficient) is 0.9120. The results show that FTIR spectra combined with siPLS-GA-PLS algorithm can be used successfully to analyze leaf nitrogen concentration of rice.