In the fabrication of a thermally driven rotary nanomotor with the dimension of a few nanometers, fabrication and control precision may have great influence on rotor's stability of rotational frequency (SRF). To investigate effects of uncertainty of some major factors including temperature, tube length, axial distance between tubes, diameter of tubes and the inward radial deviation (IRD) of atoms in stators on the frequency's stability, theoretical analysis integrating with numerical experiments are carried out. From the results obtained via molecular dynamics simulation, some key points are illustrated for future fabrication of the thermal driven rotary nanomotor.