Recent advanced experimental implementations of optical lattices with highly tunable geometry open up new regimes for exploring quantum many-body states of matter that had not been accessible previously. Here we report that a topological fermionic superfluid with higher Chern number emerges spontaneously from s-wave spin-singlet pairing in an orbital optical lattice when its geometry is tuned to explicitly break reflection symmetry. Qualitatively distinct from the conventional scheme that relies on higher partial wave pairing, the crucial ingridient of our model is topology originating from mixing higher Wannier orbitals. It leads to unexpected changes in the topological band structure at the single-particle level, i.e. the bands are transformed from possessing two flux π Dirac points into a single quadratic touching point with flux 2π. Based on such engineered single-particle bands, spin-singlet pairing of ultracold fermions arising from standard s-wave attractive interaction is found to induce higher Chern number (Chern number of 2) and topologically-protected chiral edge modes, all occurring at a higher critical temperature in relative scales, potentially circumventing one of the major obstacle for its realization in ultracold gases.