The invention discloses a potential energy surface scanning method and system for molecular conformation space analysis. The method comprises the steps that whether molecules have adjacent dihedral angles or not is judged; if an adjacent dihedral angle exists, whether the adjacent dihedral angles are coupled or not is judged through QM calculation, if not, one-dimensional potential energy scanningis conducted, and if coupling is judged, MM coupling judgment is conducted; if MM calculation judges that the adjacent dihedral angles are not coupled, one-dimensional potential energy surface scanning is carried out; if MM calculation judges that the adjacent dihedral angles are coupled, a step of calculating the coverage of the extreme point combination obtained by scanning the one-dimensionalpotential energy surfaces of the two dihedral angles on the extreme points on the two-dimensional potential energy surfaces according to the scanning result of the MM is performed; if the coverage degree is good, one-dimensional potential energy surface scanning is carried out; according to the scanning method and system, different conformation scanning methods are adopted for different moleculesaccording to conditions, the flexibility is high, the calculation efficiency can be considered, the accuracy can be guaranteed, important conformations in a molecular conformation space can be reserved to the maximum extent, and the scanning result can reflect the conformation space of the molecules more accurately.