Multiscale problems can usually be approximated through numerical homogenization by an equation with some effective parameters that can capture the macroscopic behavior of the original system on the coarse grid to speed up the simulation. However, this approach usually assumes scale separation and that the heterogeneity of the solution can be approximated by the solution average in each coarse block. For complex multiscale problems, the computed single effective properties/continuum might be inadequate. In this paper, we propose a novel learning-based multi-continuum model to enrich the homogenized equation and improve the accuracy of the single continuum model for multiscale problems with some given data. Without loss of generalization, we consider a two-continuum case. The first flow equation keeps the information of the original homogenized equation with an additional interaction term. The second continuum is newly introduced, and the effective permeability in the second flow equation is determined by a neural network. The interaction term between the two continua aligns with that used in the Dual-porosity model but with a learnable coefficient determined by another neural network. The new model with neural network terms is then optimized using trusted data. We discuss both direct back-propagation and the adjoint method for the PDE-constraint optimization problem. Our proposed learning-based multi-continuum model can resolve multiple interacted media within each coarse grid block and describe the mass transfer among them, and it has been demonstrated to significantly improve the simulation results through numerical experiments involving both linear and nonlinear flow equations.