Learning the flows of hybrid systems that have both continuous and discrete time dynamics is challenging. The existing method learns the dynamics in each discrete mode, which suffers from the combination of mode switching and discontinuities in the flows. In this work, we propose CHyLL (Continuous Hybrid System Learning in Latent Space), which learns a continuous neural representation of a hybrid system without trajectory segmentation, event functions, or mode switching. The key insight of CHyLL is that the reset map glues the state space at the guard surface, reformulating the state space as a piecewise smooth quotient manifold where the flow becomes spatially continuous. Building upon these insights and the embedding theorems grounded in differential topology, CHyLL concurrently learns a singularity-free neural embedding in a higher-dimensional space and the continuous flow in it. We showcase that CHyLL can accurately predict the flow of hybrid systems with superior accuracy and identify the topological invariants of the hybrid systems. Finally, we apply CHyLL to the stochastic optimal control problem.