Atomically precise graphene nanoflakes called nanographenes have emerged as a promising platform to realize carbon magnetism. Their ground state spin configuration can be anticipated by Ovchinnikov-Lieb rules based on the mismatch of π electrons from two sublattices. While rational geometrical design achieves specific spin configurations, further direct control over the π electrons offers a desirable extension for efficient spin manipulations and potential quantum device operations. To this end, we apply a site-specific dehydrogenation using a scanning tunneling microscope tip to nanographenes deposited on a Au(111) substrate, which shows the capability of precisely tailoring the underlying π-electron system and therefore efficiently manipulating their magnetism. Through first-principles calculations and tight-binding mean-field-Hubbard modeling, we demonstrate that the dehydrogenation-induced Au-C bond formation along with the resulting hybridization between frontier π orbitals and Au substrate states effectively eliminate the unpaired π electron. Our results establish an efficient technique for controlling the magnetism of nanographenes.