It is generally accepted that the convenient fabrication of a metal phthalocyanine-based heterogeneous catalyst with superior catalytic activity is crucial for its application. Herein, a novel and versatile ultrasonic-assisted biosynthesis approach (conducting ultrasonic treatment during biosynthesis process) was tactfully adopted for the direct immobilization of a sulfonated cobalt phthalocyanine (PcS) catalyst onto a graphene–bacterial cellulose (GBC) substrate without any modification. The prepared phthalocyanine–graphene–bacterial–cellulose nanocomposite, PcS@GBC, was characterized by field emission scanning electron microscope (FESEM) and X-ray photoelectron spectroscopy (XPS). The catalytic activity of the PcS@GBC was evaluated based on its catalytic oxidation performance to dye solution, with H2O2 used as an oxidant. More than a 140% increase of dye removal percentage for the PcS@GBC heterogeneous catalyst was found compared with that of PcS. The unique hierarchical architecture of the GBC substrate and the strong interaction between PcS and graphene, which were verified experimentally by ultraviolet-visible light spectroscopy (UV-vis) and Fourier transform infrared spectroscopy (FT-IR) and theoretically by density functional theory (DFT) calculation, were synergistically responsible for the substantial enhancement of catalytic activity. The accelerated formation of the highly reactive hydroxyl radical (·OH) for PcS@GBC was directly evidenced by the electron paramagnetic resonance (EPR) spin-trapping technique. A possible catalytic oxidation mechanism for the PcS@GBC–H2O2 system was illustrated. This work provides a new insight into the design and construction of a highly reactive metal phthalocyanine-based catalyst, and the practical application of this functional nanomaterial in the field of environmental purification is also promising.