Achieving highly stable temperature control is essential for cryostats. However, the cryocooler used in cryostats, such as the pulse tube cryocooler, produces regular sinusoidal temperature fluctuations due to its inherent working principles. To establish a highly stable temperature environment, an active phase and amplitude control method for suppressing temperature fluctuation is proposed in this paper, by which the optimal phase and amplitude can be predicted in theory. To validate this approach, a thermal response model was developed based on experiments conducted in the thermodynamic temperature international comparison cryostat at approximately 3.7 K. Based on this model, we conducted both single-stage and multi-stage active temperature control experiments. The results demonstrate that the temperature control effect is the best when the active temperature control current is added at the second cold head, the fluctuation of the comparison copper block from 3.3mK to 0.166mK with 94.9 % suppression rate. The multi-stage joint temperature control reduced the temperature fluctuation with an attenuation rate of 95.4 %. These findings offer significant potential for improving temperature stability in future thermodynamic temperature comparison experiments.