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With finite element simulation, the time dependent thermoelectric performance of silicon nanowires (SiNWs) is studied systematically. Short response time has been observed in SiNW cooler which decreases with increasing of the number of SiNWs. Moreover, the impacts of inhomogeneous thermal conductivity distribution in one bundle on the cooling temperature have been studied. The cooling temperature decreases due to the existing of unexpected high thermal conductivity SiNW. This impact can be suppressed in large system. Our results provide a comprehensive performance analysis of SiNWs for on-chip thermoelectric cooler applications.