In order to meet the requirements of large downward force and high stiffness performance for the friction stir welding process, this paper proposes a 5 degree-of-freedom hybrid manipulator as friction stir welding robot. It is composed of a 3 degree-of-freedom redundant parallel module and a 2 degree-of-freedom rotating head. Semi-analytical stiffness model of the hybrid manipulator is firstly established by compliance models of the two substructures. Virtual work principle, deformation superposition principle and twist/wrench mapping model are applied to this compliance modeling process. A novel instantaneous stiffness performance index is then proposed on the basis of instantaneous energy defined by reciprocal product of external payload screw and corresponding deformation screw. It solves the problems of inconsistent physical unit of linear/angular stiffness and is able to evaluate overall and worst-case stiffness performance. Next, stiffness/compliance experiments are carried out to verify the stiffness model and the novel instantaneous stiffness performance index. Finally, stiffness performance of 5 degree-of-freedom hybrid manipulator is thoroughly discussed in terms of engineering requirements, worst-case stiffness performance and stiffness singularities. It can be summarized that the semi-analytical stiffness model and the novel instantaneous stiffness index are effective in analyzing and evaluating stiffness performance of the 5 degree-of-freedom hybrid manipulator.