On the basis of designing and implementation of heterogeneous dual computer fault-tolerant system architecture, a Markov based system availability evaluation model is proposed to address the problems of how to evaluate and estimate the availability index of such high availability system. Through evaluation model we analyze the system's availability, estimate the availability index, and prove the superiority of such heterogeneous system by comparing it with stand-along system and homogeneous dual computer system. The estimation and comparative analysis results shows that, such evaluation model evaluate the system's availability effectively, and prove the system can meet the requirements of five 9s high availability index. Also, the paper sums up two main factors which impact the availability of heterogeneous dual computer fault-tolerant system, one is the mean time between failure and the other is system's total repair time.