A specific variable selection method was proposed based on three-step hybrid strategy for near infrared spectral analysis. By analyzing functions of each step and characteristics of various variable selection methods, synergy interval partial least squares, iterative variable subset optimization and bootstrapping soft shrinkage were chosen for three steps. To test effect of the three-step hybrid method, it was applied into corn and soil spectral data and compared to other common methods. Results showed that three-step hybrid variable selection method selected 1% variables of full spectrum, calibration determination coefficient and prediction determination coefficient reached 0.9976 and 0.9932. It could effectively extract variables related to tested substance and provide a new variable selection method for near infrared spectral analysis.