Harvest time and storage time had significant effects on nutrient quality and Volatile Organic Compounds (VOCs) of alfalfa. The objective of this study was to use headspace solid-phase microextraction gas chromatography-mass spectrometry (HS-SPME-GC-MS) to analyze alfalfa at different harvest periods (budding stage, early blooming, full blooming), and storage for 0 d, 90 d, 180 d, 270 d, and 360 d, the dynamic changes in VOCs and nutritional quality. Results indicated that ketones, aldehydes, alcohols and esters were the main volatile components of alfalfa VOCs, accounting for 87.41%, 88.57% and 90.85% of the total volatile components at budding stage, early blooming and full blooming, respectively. VOCs and nutrient quality of alfalfa varied significantly in different harvest periods; delayed harvesting significantly reduced alfalfa aldehydes, alcohols, crude protein (CP), and total digestible nutrients (TDN) and significantly increased ketone, dry matter (DM), acid detergent fiber (ADF) and neutral detergent fiber (NDF) contents (p < 0.05). After Comprehensive consideration ofthe yield, nutritional quality and VOCs of alfalfa, the best harvest time was determined to be the budding stage. The VOCs and nutrient quality of alfalfa were significantly different at different storage durations, and ketones, ADF and NDF were significantly increased and significantly reduced DM, CP and TDN (p < 0.05). Ketone content and neutral detergent fiber (NDF) content had a significant positive correlation, (NDF F = 5.5, p = 0.024). Storage 360 d 2-methylbutyraldehyde (musty), 1-octen-3-one (earthy musty odor) content increased. These may be the key compounds that causes the smell of fresh alfalfa to fade away and a musty smell to emerge.