Rapeseed oil is a widely consumed edible oil that contains varieties of beneficial micronutrients such as tocopherols and phytosterols; however, the high acid value due to increased free fatty acid can imperil the oil quality and safety. This paper proposed the enzymatic deacidification for high-acid rapeseed oil and simultaneous production of functional diacylglycerols (DAGs) catalyzed by self-made immobilized lipase CALB@MCM-41-C8. The results indicate that the carrier of molecular sieve MCM-41 exhibited a sufficient surface area of 1439.9 m2/g and a proper pore size of 3.5 nm, promoting the immobilization of lipase CLAB. Under the optimal reaction conditions, the acid value of rapeseed oil was largely decreased from 15.3 mg KOH/g to 1.7 mg KOH/g within 3 h, while DAG content was increased from 1.2% to 40.2%. The antioxidant stability of rapeseed oil was also increased from 4.3 h to 7.6 h after enzymatic deacidification. Besides, the deacidified rapeseed oil exhibited fatty, bitter almond aromas, compared to the picked-vegetable, spicy, and pungent aromas for high-acid oil. Finally, the catalytic stability and applicability of CALB@MCM-41-C8 was validated, thus demonstrating the great potential of CALB@MCM-41-C8 in green refining of edible oils and sustainable synthesis of functional lipids.