The objective of this study was to investigate the effect of protein oxidation on microbial, free amino acids (FAAs) and biogenic amines (BAs) in Chinese dry sausage during processing. Three different batches of Chinese dry sausages were examined: control batch, pro-oxidation batch and anti-oxidation batch. The experimental results revealed that anti-oxidation batch showed the lowest degree of protein oxidation compared with control batch, while the results of the pro-oxidation batch were just opposite. With the increasing protein oxidation, estimated by protein carbonyls and sulfhydryls, microbial content and free amino acid content increased, while BA content decreased. The protein carbonyls were positively correlated with total FAAs (P < 0.01) and total BA content (P < 0.05), while sulfhydryls content was negatively correlated with total FAA content (P < 0.01), total viable counts (P < 0.01), and total BA content (P < 0.01). In conclusion, reduced protein oxidation contributes to improved quality of Chinese dry sausage. This research provided a new strategy to improve the quality of meat product manufacture.