Taking nitroxide radicals as spin sources, we explore the intramolecular magnetic coupling interactions of the trans- and cis-forms of benzylideneaniline (BA)-bridged diradicals, in which the central –CHN– unit can undergo single protonation to convert to its protonated counterpart or vice versa. The calculated results for these two pairs of diradicals (protonated versus unprotonated trans and cis forms) verify that the signs of their magnetic coupling constants J do not change, but the magnitudes significantly increase after protonation. In the structure, the better conjugation of the protonated trans diradical and two reduced CCNC and CCCN torsion angles of the protonated cis one make for a more efficient spin transport, promoting the spin polarization, thus leading to larger spin couplings. In terms of mechanism, the proton-induced magnetic enhancement should be attributed to strong participation of the coupler BA through its lowest unoccupied molecular orbital (LUMO) with a lower energy level after protonation, and the small HOMO–LUMO (HOMO: highest occupied molecular orbital) gap of the coupler BA through protonation is crucial in explaining such remarkable spin-coupling enhancement. Furthermore, different linking modes of the radical groups to the couplers are also considered to confirm our conclusions. In addition, we also make a comparison of the magnetic coupling strengths among their isoelectronic analogues of BA-, AB- and stilbene-bridged nitroxide diradicals before or after protonation, and find a linear correlation among them. It should be noted that the magnetic behaviors of all these diradicals obey the spin alternation rule and singly occupied molecular orbital (SOMO) effect. This work provides helpful information for the rational design of promising magnetic molecular switches.