The effects of microwave, baking, roasting, and steaming treatments as different thermal processing methods on the nutritional and functional qualities of black soybeans were investigated. Specifically, the treatment effects on anti-nutritional factors, bioactive components, protein structure and solubility, and the grindability of the raw material were analyzed to identify the optimal processing method. Additionally, response surface methodology was used to optimize the soybean maturation process, with the anthocyanin content used as the evaluation index. The microwave treatment resulted in black soybean powder with the smallest average particle size (22.49 μm) and a uniform distribution as well as the highest β-sheet content (33%) in the protein secondary structure. Moreover, the protein solubility in potassium hydroxide was found to be comparable to that of the roasted sample (~70%). Additionally, the retention of anthocyanins (41.44 mg/100 g), proanthocyanidins (1.43 μg CAE•g-1), total phenolics (3.54 mg GAE•g-1), and total flavonoids (3.41 mg CAE•g-1) by the microwave-treated soybeans was significantly higher than that observed under the other treatments. According to the response surface methodology results, the optimal microwave processing conditions were a heating time of 6 min, power of 807 W, and sample load of 147 g, under which the anthocyanin content reached 47.29 mg/100 g. Compared with the other maturation methods, microwave treatment exhibited significant advantages in enhancing the grindability of black soybeans and improving their retention of bioactive compounds.