With the aim of preparing a sulfonic acid-type solid acid catalyst having a high density of acid sites and excellent stability, this work synthesized sulfonic acid bowl-shaped hydrothermal carbon microspheres (SA-OBHCs), using amine groups as the primary sulfonic acid bonding sites. This material was synthesized via a three-step functionalization process comprising the oxidation, amidation and sulfonation of BHCs. The extent to which chlorosulfonic acid reacted with amine groups in diethylenetriamine molecules on microsphere surfaces was also investigated using density functional theory calculations. These calculations showed that the substitution reaction of primary amines proceeded less readily than that of secondary amines but provided a more stable product. The surface acid density of the SA-OBHCs was as high as 11.2 mmol·g−1 and the –SO3H groups on the SA-OBHCs were found to be thermally stable up to 200 °C. These SA-OBHCs were subsequently used to catalyze the synthesis of fatty acid methyl esters (FAMEs) from a waste frying oil model compound and methanol. Reactions performed using a methanol/oil molar ratio of 20:1 at 140 °C for 3 h gave a FAMEs yield of 93.4 %. After four reuses, an SA-OBHCs specimen provided a FAMEs yield of 77.5 %, demonstrating the significant stability of this material.