The Green Food apple production has increased rapidly in China recently, due to its sustainability and high-quality compared to the conventional apple. The aim of this study was evaluating and comparing physicochemical quality as well as metabolomics of the apples grown in green certified and conventional production systems. The results of physicochemical properties indicated that Green Food apples showed significant superiorities than conventional ones at soluble solids content, firmness and titratable acidity. While, in the vitamin C content comparison, there was no significant difference. Compounds, including several phenolic compounds and fatty acids, were revealed by the untargeted metabolomics as differential markers between apples grown in the two production systems, and could serve as the potential markers for differentiating these two types of apples. Overall, these results of this study could encourage the Green Food apples consumption, promote its production, and will benefit the development of Green Food production and the cleaner agricultural production in China.