With the wide application of wireless sensor network, the security mechanism based on cryptography faces many challenges in computational complexity and security, and physical layer secret key extraction as an alternative solution has been widely studied. To meet the requirements of high key generation rate (KGR) and low key disagreement rate (KDR) in the secret key extraction process, an improved channel quantization alternating (CQA) algorithm is proposed in this paper. The algorithm filtrates the phase values of channel frequency response (CFR) using test results of CFR amplitude values, and then quantizes the reserved phase values by CQA algorithm. Compared to the existing CQA algorithm and improved channel quantization with guard-band (CQG) algorithm, simulation results show that the KDR of the proposed algorithm decreases by 31.5% and 20.4%, and the KGR decreases by 5.4% and increases by 5.2%, respectively. The proposed algorithm improves the KGR while ensuring a low KDR, and the extracted secret key passes the NIST test.