A biologically microscopic system presenting a highly scientific interest is the microtubule (MT). Our research endeavor revolves around the eigenfrequencies’ analysis of an MT embedded in the cytoplasm of the cell by means of the nonlocal integral elasticity for the first time. The MT is simulated as a beam and the cytoplasm as a Pasternak-type elastic foundation, respectively. The responses of the nonlocal integral stress models show to have a softening behavior in comparison with that of the classic model. Unlike the nonlocal differential model, no paradoxes and inconsistencies are raised for the nonlocal integral models. Our research conclusions are a hopeful sign for the applications of biomaterials and bioengineering structures.