A series of 2D layered isostructural coordination complexes {[M3(L)2(H2O)6]·H2O}n (M = Mn (1), Mn0.7Co0.3 (2), Mn0.5Co0.5 (3), Mn0.3Co0.7 (4), and Co (5), respectively, H3L = 1-aminobenzene-3,4,5-tricarboxylic acid) have been synthesized under hydrothermal conditions, and applied to catalyze the reaction of degenerating organic dyes under visible light irradiation. The photocatalytic results indicate that complex 5 exhibits good photocatalytic properties in the presence of H2O2, while 1 can restrain the photodegradation of organic dyes. Remarkably, when Mn ions are gradually replaced by Co ions in the complexes, the photocatalytic activities of 1–5 turn from inhibition to promotion, which is a controllable regulation of photocatalytic properties via changing metal ions. Moreover, by using novel magnetic analysis methods and diffuse-reflectance UV/Vis spectra analysis methods, we explain the influence of central metal ions on the photocatalytic performance.