We investigate quasi-particle excitation modes and the topological number of a fractional-flux quantum vortex in a layered (multi-component) superconductor. The Bogoliubov equation for a half-flux quantum vortex is solved to show that there is no low-lying Andreev bound state near zero energy in the core of a quantum vortex, which is surprisingly in contrast to the result for an inter-flux vortex. Related to this result, there are singular excitation modes that have opposite angular momenta, moving in the opposite direction around the core of the vortex. The topological index (skyrmion number) for a fractional-flux quantum vortex becomes fractional since the topological index is divided into two parts where one from the vortex (bulk) and the other from the kink (domain wall, boundary). The topological numbers for both the vortex and the kink (domain wall) are fractional, and their sum becomes an integer. This shows an interesting analogy between this result and the index theorem for manifolds with boundary. We argue that fractional-flux quantum vortices are not commutative each other and follow non-abelian statistics. This non-abelian statistics of vortices is different from that in p-wave superconductors.