We investigate vortex partition functions defined from integrals over the handsaw quiver varieties of type A1 via wall-crossing phenomena. We consider vortex partition functions defined by two types of cohomology classes, and get functional equations for each of them. We also give explicit formula for these partition functions. This gives proofs to formula suggested by physicsts. In particular, we obtain geometric interpretation of formulas for multiple hypergeometric functions including rational limit of the Kajihara transformation formula.