To improve insufficient taste and imbalanced aroma of enzyme-modified cheese (EMC), pre-enzymolysis followed by lactic acid bacteria (LAB) fermentation was employed in this study. The strategy generated taste compounds by fermentation and released crucial flavor precursors by pre-enzymolysis. Flavor precursors and flavor compounds from each step were measured. Results showed that 45–50 and 15–17 times higher free amino acid (FAA) and free fatty acid (FFA) flavor precursors than the control were respectively achieved based on acceptable bitterness and soapiness during pre-enzymolysis. Pre-proteolysis accelerated fermentation and increased lactic acid, floral and almond aromatic ring compounds from phenylalanine (2.0–15.7 times), and rancid branched acids from leucine (3.2–4.4 times) during fermentation. Pre-lipolysis released massive methyl ketones and fatty acids, but flavor imbalanced, which was improved by promoting short-chain fatty acid production during fermentation. These results provided practical references for producing EMC with authentic Cheddar flavor and new avenues for flavor improvement of EMC.