We develop a topological theory for fault-tolerant quantum computation in quantum low-density parity-check (qLDPC) codes. We show that there exist hidden simplicial or CW complex structures encoding the topological data for all qLDPC and CSS codes obtained from product construction by generalizing the Freedman-Hastings code-to-manifold mapping. This is achieved by building manifolds from the Tanner graphs of the skeleton classical or quantum codes, which further form a product manifold and an associated thickened product code defined on its triangulation. One can further deformation retract the manifold back to a CW complex which supports a non-topological code with minimal overhead suitable for near-term implementation. Both types of codes admit cohomology operations including cup product which can induce non-Clifford gates. When applying this mapping to a 3D hypergraph product code obtained from the product of 3 copies of good classical expander codes, we obtain non-Clifford logical CCZ gates via constant depth circuits on a code with constant stabilizer weight $w=O(1)$, constant rate $K=Θ(N)$, and polynomial distance $D=Ω(N^{1/3})$. When applied to logical CCZ on 3D homological product codes consisting of the product of a pair of good quantum and classical LDPC codes, we can further improve the distance to $D=Ω(\sqrt{N})$ exceeding the $N^{1/3}$ distance barrier implied by the Bravyi-König bound for conventional topological codes with the aid of non-Euclidean geometries. Our work suggests that it is feasible to apply native logical non-Clifford gates on qLDPC codes or directly inject high-fidelity magic states as resources ('magic state fountain') without the distillation process. For the homological product construction, the fountain can inject $Θ(\sqrt{N})$ magic states in parallel in a single round.