The super-harmonic resonance of the nonlinear torsional vibration of misaligned rotor system driven by universal joint was studied considering both natural structure misalignment and actual error misalignment. Utilizing multi-scale method, the periodic solution of weakly nonlinear torsional vibration equation was obtained corresponding to super-harmonic resonance, including amplitude-frequency and phase-frequency characteristic expressions of steady periodic solution. The stability of equilibrium point was investigated using Lyapunov first approximate stability theory, then the stable region and unstable region on the amplitude of the super-harmonic resonance periodic solution, which varied with the detuning parameter. At last, the driving shaft’s steady periodic motion of the first approximation and its calculation simulation were carried out according to the kinetic relation about driven shaft and driving shaft. It is found that jumping phenomenon and dynamic bifurcation occur when the rotating angular velocity of driving shaft is half of the natural frequency of the deriving system. The results above indicate the fundamental characteristic of the nonlinear dynamic on the misaligned rotor, also applying the foundation for advanced bifurcation and singularities analysis.