In order to analyze the channel estimation performance of near space high altitude platform station (HAPS) in wireless communication system, the structure and formation of HAPS are studied in this paper. The traditional Least Squares (LS) channel estimation method and Singular Value Decomposition-Linear Minimum Mean-Squared (SVD-LMMS) channel estimation method are compared and investigated. A novel channel estimation method and model are proposed. The channel estimation performance of HAPS is studied deeply. The simulation and theoretical analysis results show that the performance of the proposed method is better than the traditional methods. The lower Bit Error Rate (BER) and higher Signal Noise Ratio (SNR) can be obtained by the proposed method compared with the LS and SVD-LMMS methods.