For current problems in personnel performance evaluation model such as neglect of elementary condition, using absolute performance scale, lack of relative standard, focusing too much on shortterm performance, according as characters of innovation and R&D personnel performance, this paper designs index system of innovation performance evaluation, which reflects R&D personnel’s effort degree and potential level. Taking innovation performance as the main factor of evaluation, the evaluation model is constructed to measure impersonally R&D personnel’s innovation performance. Finally the model is applied in a sample of three hundred R&D personnel from a largescale manufacturing enterprise. Effort index, potential index, excellence level and error level of each personnel are evaluated as the basis of comprehensive evaluation for R&D personnel’s performance.