In this work, axial vibration of nanorod was analyzed based on two phase integro-differential nonlocal elasticity theory using isogeometric method. Two phase integro-differential nonlocal elasticity theory not only shows the nonlocal property in an integrated manner based on kernel weight function, but also combines local and nonlocal linear curvature for a two phase nonlocal elastic material. The new isogeometric approach combines finite element method with computational geometry and can present an accurate geometric model for the problem. Also, using b-spline basis functions with arbitrary continuity order, it can be a better alternative for classical finite element methods. The obtained results indicated that isogeometric approach was superior to finite element method in term of speed and convergence quality. Moreover, in this model, the effects of phase and nonlocal parameters on the natural frequencies of the nanorod were investigated and it was shown that increase of parameters of local phase and nonlocal length scale, respectively, increased and decreased the values of natural frequencies of nanorods. Finally, for two special cases, asymptotic frequencies for a single type of nonlocal rod, two phase integro-differential was obtained and the results were compared with corresponding available differential Eringen results.