The aim of this paper is to extend the Morse theory for geodesics to the conical manifolds. In a previous paper we defined these manifolds as submanifolds of R-n with a finite number of conical singularities. To formulate a good Morse theory we use an appropriate definition of geodesic, introduced in the cited work. The main theorem of this paper (see Theorem 3.6, section 3) proofs that, although the energy is nonsmooth, we can find a continuous retraction of its sublevels in absence of critical points. So, we can give a good definition of index for isolated critical values and for isolated critical points. We prove that Morse relations hold and, at last, we give a definition of multiplicity of geodesics which is geometrical meaningful. In section 5 we compare our theory with the weak slope approach existing in literature. Some examples are also provided