A reliability enhancement algorithm for Physical Unclonable Function （PUF） was proposed to address the instability of PUF’s response caused by external and internal factors. The proposed algorithm is based on the Non-Orthogonal Discrete （NOD） transform. Firstly， a reorder mixer was designed to iteratively process the random seed vector and PUF response， resulting in the inner product of the non-orthogonal confusion matrix and the response confusion matrix， upon which the NOD spectrum was established. The algorithm effectively solved the bias of key caused by insufficient uniformity of PUF. Then， the partition encoding and decoding strategy enabled the NOD spectrum to have the ability to tolerate certain errors， significantly improving the reliability of the final response by limiting the impact of unstable responses to a limited range. Compared to traditional error correcting code-based methods， the proposed algorithm requires fewer auxiliary data. Experimental results on SRAM-XMC dataset show that， during 101 repeated experiments with 2 949 120 sets of 64-bit responses， the average reliability of the proposed algorithm reaches 99.97%， the uniqueness achieves 49.92%， and the uniformity reaches 50.61%. The experimental results demonstrate that the proposed algorithm can effectively improve reliability while ensuring uniformity and uniqueness of PUF responses.