Glutathione (GSH) conjugation was an important pathway to regulate the toxicity of microcystins (MCs) targeted to protein phosphatases. To explore the specific molecular mechanism for GSH detoxification, two typical MC-GSHs (derived from MCLR and MCRR) were synthesized, prepared, and purified according to previous research. Then, the reduced inhibition effect for MC-GSHs on protein phosphatase 1 was verified by comparing with their original toxins. To further clarify the molecular mechanism for MC-GSHs detoxification, we evaluated the interactions between MCs/MC-GSHs and PP1 with the assistance of MOE molecule simulation. When GSH was introduced to MCs, the covalent binding (Mdha 7 to Cys 273), the hydrophobic interaction (Adda 5 with PP1), the hydrogen bonds (especially for Lys 2-Arg 96 and Glu 6-Tyr 272), the covalent combination (between Mdha 7 and Cys 273), and the ion bonds (between Mn 2+ and Asn 124/His 248/Asp 64/His 66) of MCLR/MCRR-PP1 complexes weakened to a certain extent, while the ion bonds between Mn 2+ and His 173/Asp 92 residues increased. It was not difficult to find that the toxicity of MCs was closely related to the above sites/interactions and the above key information for MCs-PP1; MC-GSHs-PP1 complexes were important for clarifying the detoxification mechanism of MC-GSHs pathway. This study offers a comprehensive cognition on MCs toxicity regulation and provides valid theoretical support to control their potential risk.