Considering the former attack algorithm was impacted by noise easily, a trace driven data Cache timing attack model on RSA was built, and the analysis algorithm of the power exponent was provided based on the Cache hit or miss side channel information. This paper proposes a new algorithm for automated analysis of the abundant Cache timing data based on these, which combines the vector quantization and Hidden Markov Model (HMM) cryptanalysis. We built a template for Cache timing analysis, and get the operation sequence using the Viterbi algorithm with HMM, to improve the precise of analysis. Finally, under the practical environment, we realized a Cache timing attack on RSA of OpenSSL. The experiment results showed that: the proposed analysis algorithm can effectively reduce the influence of noises from other processes, make the analysis of Cache timing data automatically, and the effectiveness and feasibility of Cache timing attack on RSA also can be improved.