Phytic acid modified graphene oxide (PGO) has encouraging prospect in environmental application. Herein, PGO was fabricated with a simple hydrothermal method and used as adsorbent to remove methyl blue (MB). Elaborate inspection based on the hard-soft acid-base (HSAB) principle, spectroscopic characterization, as well as batch adsorption and fitting were conducted to unravel the adsorption mechanism. Results show, PGO efficiently adsorbs 89.08 mg·g−1 of MB in 22 min. HSAB principle proposes, high electron transfer (ΔN) and energy lowering (ΔE) induce covalent bond (chemical interaction), while low ΔN and ΔE induce electrostatic effect (physical interaction). Accordingly, both the first and second strongest interaction occurs between PA moiety and MB: π electrons of MB flows towards O atom in OH and O(–O–) of PA, respectively. Yet the third strongest interaction happens between GO moiety and MB: electron of O atom in OH group of GO flows towards N atom of MB. Above top three interactions are characterized by prominent ΔN and ΔE implying the formation of covalent bond. However, other interactions yield low ΔN and ΔE, suggesting the presence of electrostatic effect. HSAB principle conclusion was substantiated by FTIR and UV–Vis analyses. These findings confirm that PA modification enhances the adsorption affinity of graphene oxide. Thereby, chemical adsorption induced by physical interaction is proposed. This work may inspire the design of efficient adsorbent based on PGO framework for environmental restoration.