Abstract: In recent years, food waste has become a global research topic, and fruit loss and waste is an important component of food waste. From the place of origin to the table, fruit waste occurs during picking, post-harvest processing, storage, circulation, consumption, and other stages with varying degrees of loss. Therefore, it is necessary to study the loss and waste of the whole fruit industry in China and to analyze the impact of its resources on the environment. The purpose of this study is to provide data to reduce the loss and waste of fruit and improve the utilization efficiency of ecological resources. Using apples and citrus as examples, this study investigated all of the links in the whole fruit industry chain via questionnaires and field visits. The total amount of loss and waste was estimated, including the ecological, carbon, and water footprints using key parameters, such as greenhouse gas emissions and water waste. A field survey was conducted in the main fruit marketing area to investigate and analyze the loss and waste of fruit during production, post-harvest treatment, storage, circulation, and consumption. This included 209 workers in the entire industrial chain in the main producing area and 271 consumers in the main selling area. The results showed that the wastage rates of apples and citrus were 18.56% and 17.15%, respectively, among which the wastage rate of the circulation link was the highest, accounting for approximately one-third of the total wastage. The wastage for apples and citrus were 719.86×10⁴ t and 733.99×10⁴ t, respectively, for a total loss of 1453.85×10⁴ t. The ecological footprint of apple and citrus wastage was 13.33×10⁴ hm² and 13.76×10⁴ hm², respectively, and the total ecological footprint was 26.09×10⁴ hm². The carbon footprint was 92.37×10⁴ t (CO₂ eq) and 102.98×10⁴ t (CO₂ eq), respectively, and the total carbon footprint was 195.35×10⁴ t (CO₂ eq). The water footprint was 57.65×10⁸ m³ and 41.10×10⁸ m³, respectively, and the total water footprint was 98.75×10⁸ m³. During circulation, jolting, bumping, and squeezing could damage the fruit, resulting in loss; the highest in the entire supply chain. Bumps and squeezes during transportation were the main reasons for loss. Improper selection and temperature control by consumers during sales also caused fruit spoilage. The highest carbon emissions from production accounted for more than 90% of the carbon footprint, mainly due to the application of pesticides and fertilizers. To reduce fruit loss and waste and to improve the utilization efficiency of resources, some measures could be taken, such as improving the mechanization and standardization of fruit production levels and reducing the use of chemical fertilizers and pesticides. In the circulation process, operators must keep the environment clean and tidy. Moreover, an entirely cold-chain process should be advocated, and waste should be opposed during consumption.