A local refinement hybrid scheme (LRCSPH-FDM) is proposed to solve the two-dimensional (2D) time fractional nonlinear Schrdinger equation (TF-NLSE) in regularly or irregularly shaped domains, and extends the scheme to predict the quantum mechanical properties governed by the time fractional Gross–Pitaevskii equation (TF-GPE) with the rotating Bose–Einstein condensate. It is the first application of the purely meshless method to the TF-NLSE to the author’s knowledge. The proposed LRCSPH-FDM (which is based on a local refinement corrected SPH method combined with FDM) is derived by using the finite difference scheme (FDM) to discretize the Caputo TF term, followed by using a corrected smoothed particle hydrodynamics (CSPH) scheme continuously without using the kernel derivative to approximate the spatial derivatives. Meanwhile, the local refinement technique is adopted to reduce the numerical error. In numerical simulations, the complex irregular geometry is considered to show the flexibility of the purely meshless particle method and its advantages over the grid-based method. The numerical convergence rate and merits of the proposed LRCSPH-FDM are illustrated by solving several 1D/2D (where 1D stands for one-dimensional) analytical TF-NLSEs in a rectangular region (with regular or irregular particle distribution) or in a region with irregular geometry. The proposed method is then used to predict the complex nonlinear dynamic characters of 2D TF-NLSE/TF-GPE in a complex irregular domain, and the results from the posed method are compared with those from the FDM. All the numerical results show that the present method has a good accuracy and flexible application capacity for the TF-NLSE/GPE in regions of a complex shape.