With the rapid advancement of unmanned aerial vehicle (UAV), ensuring the security of communication links among UAVs has become crucial. In this paper, we propose a novel physical layer key generation scheme based on channel codeword reconstruction. In UAV communications, the high mobility of aerial nodes leads to short channel coherence time, which together with noise causes inevitable channel estimation errors. These errors significantly degrades the performance of wireless channel-based key generation. Therefore, we propose a codeword construction algorithm that achieves a polarization characteristic, which effectively segregates reliable keys from unreliable ones. Compared to the existing quantization-based key generation scheme, our approach maximize the utilization of raw channel information and employ soft-decision decoding to generate key. Simulation results demonstrate that the proposed scheme reduces the key disagreement rate for legitimate users and increases the number of consistently generated keys. Furthermore, our method ensures a lower key consistency rate for eavesdropper, which guarantees system security.