A mathematical model of polymerase chain reaction (PCR) containing uncertain and time-varying parameters has become important for model-based guidance experiment design. In this study, the local and global sensitivity analyses were conducted to identify that the responses of PCR process vary with their parameters of initial reactant concentrations and rate constants. Our results showed that the template concentration in initial reactant concentrations had the largest effect on DNA amplification yield. The rate constant characteristics showed that the local sensitivity basically determined the specific reactions; and the global sensitivity, the non-specific reactions. Our work should be helpful for optimizing PCR experimental conditions, and determining the PCR parameter sensitivities.