Complex systems are usually composed of different physically or logically connected elements. The normal operation function of the complex systems is usually supported by normal function of each element. To accurately evaluate the probability of maintaining the function of complex systems under different earthquake intensities, a probabilistic evaluation method is proposed. The method consists of two steps: system model development based on goal-oriented (GO) methodology and post-earthquake function evaluation by Monte Carlo simulation of the system. Multi damage states and operating states of system elements are integrated into the proposed method. The feasibility and applicability of the proposed method are tested using a multi-input multi-output basic system as the exemplary system. The effectiveness of the proposed method in function-oriented seismic performance assessment of complex systems is fully demonstrated by simulation results.