The nonlinear flexible joint manipulator system with time delay was taken as the research object and the time delay was introduced to establish the system dynamics equation. The nonlinear flexible joint manipulator system was analyzed theoretically by using the multiscale method, and the normative type of Hopf bifurcation occurred in the system was obtained. The effect of time delay parameters on the system Hopf bifurcation was discussed, and the stability of its periodic solution and the generated unique limit cycle were analyzed; the results of theoretical analysis were verified by numerical calculation. The results show that the results of numerical calculation agree well with the results of theoretical analysis, which verifies the validity and feasibility of the multiscale method.