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This study investigated the physicochemical and flavor quality changes in fresh-cut papaya that was stored at 4 °C. Multivariate statistical analysis was used to evaluate the freshness of fresh-cut papaya. Aerobic plate counts were selected as a predictor of freshness of fresh-cut papaya, and a prediction model for freshness was established using partial least squares regression (PLSR), and support vector machine regression (SVMR) algorithms. Freshness of fresh-cut papaya could be well distinguished based on physicochemical and flavor quality analyses. The aerobic plate counts, as a predictor of freshness of fresh-cut papaya, significantly correlated with storage time. The SVMR model had a higher prediction accuracy than the PLSR model. Combining flavor quality with multivariate statistical analysis can be effectively used for evaluating the freshness of fresh-cut papaya.