This study proposes a novel framework of the lattice Boltzmann model for multilayer shallow water equations, considering the mass and momentum exchanges between layers (LABMSWE+). Compared with the original LABMSWE model consisting of N two-dimensional lattice Boltzmann method for shallow water equation (LABSWE) models, the new model includes 1+N LABSWE models. The singular LABSWE model with unit relaxation time is introduced to update the total water depth, and thus, the layer water depths can be obtained explicitly through the fixed layer ratios. The N-layer LABSWE models with the multiple-relaxation-time operator evolve the layer velocities. These two modules are coupled by the total water depth and depth-averaged velocities. The constructed model avoids the freely variable layer thicknesses, which is considered as the main source of the instability. In addition, the mass exchanges enable this model to simulate vertical circulation flows, which are beyond the application of the LABMSWE model. Several numerical tests are then conducted to validate the proposed model. The results show that it exactly satisfies the C-property. In addition, the central difference scheme is more stable and accurate than the upwind and nonequilibrium schemes in the computing of the mass exchanges. The numerical results have an excellent agreement with analytical solutions and reference data, while some unstable and nonphysical results are obtained by the original LABMSWE model. Moreover, the computational time is about 40%–60% of that for the MIKE3, a finite volume solver for the three-dimensional shallow water equations by the Danish Hydraulic Institute.