As it is very difficult to construct conforming plate elements and the solutions achieved with conforming elements yield inferior accuracy to those achieved with nonconforming elements on many occasions, nonconforming elements, especially Adini’s element (ACM element), are often recommended for practical usage. However, the convergence, good numerical accuracy, and high computing efficiency of ACM element with irregular physical boundaries cannot be achieved using either the finite element method (FEM) or the numerical manifold method (NMM). The mixed-order NMM with background cells for integration was developed to analyze the bending of nonconforming thin plates with irregular physical boundaries. Regular meshes were selected to improve the convergence performance; background cells were used to improve the integration accuracy without increasing the degrees of freedom, retaining the efficiency as well; the mixed-order local displacement function was taken to improve the interpolation accuracy. With the penalized formulation fitted to the NMM for Kirchhoff’s thin plate bending, a new scheme was proposed to deal with irregular domain boundaries. Based on the present computational framework, comparisons with other studies were performed by taking several typical examples. The results indicated that the solutions achieved with the proposed NMM rapidly converged to the analytical solutions and their accuracy was vastly superior to that achieved with the FEM and the traditional NMM.