The shaking incubator is an incubator which consists of shaker and heating chamber for incubating and shaking sensitive samples. It replaces two devices, reducing both time and space needed. Both the shaking mechanism and temperature chamber are regulated via microprocessors, which control all sensors for motor speed, temperature and time. It is suitable for biochemistry, microbiology and clinical laboratories in which applications require temperature and shaking treatment. This article presents a novel design of calibration method of shaking incubator by studying the essential metrological parameters of the device. The experimental results show that the calibration method presented in this article can establish the metrological traceability system of shaking incubator in China in order to ensure the accuracy and reliability of the device, which is of great importance for the quality control of the device.