Apples are abundant in essential nutrients, including a variety of minerals and vitamins, and are readily digestible and assimilated by the human body. Commonly consumed worldwide, apples are particularly diverse in their varieties. The “Black Diamond” apple from Linzhi, Tibet, stands out as a significant fresh variety. This study utilizes hyperspectral imaging and deep learning techniques to investigate the impact of room temperature storage on the quality of Linzhi “Black Diamond” apples. Specifically, we assess alterations in quality indices such as hardness, weight loss, sugar-acid ratio, as well as the content of phenolics ketones, and volatile aromatic compounds. Our findings provide detailed insights into the effects of ambient storage conditions on the sensory and nutritional quality of these distinctive apples.