Continuous-variable measurement-device-independent quantum key distribution (CV-MDI QKD) can defend all attacks on the measurement devices fundamentally. Consequently, higher requirements are put forward for the source of CV-MDI QKD system. However, the imperfections of actual source brings practical security risks to the CV-MDI QKD system. Therefore, the characteristics of the realistic source must be controlled in real time to guarantee the practical security of the CV-MDI QKD system. Here we propose a countermeasure for negative impact introduced by the actual source in the CV-MDI QKD system based on one-time-calibration method, not only eliminating the loophole induced from the relative intensity noise (RIN) which is part of the source noise, but also modeling the source noise thus improving the performance. In particular, three cases in terms of whether the preparation noise of the practical sources are defined or not, where only one of the users or both two users operate monitoring on their respective source outputs, are investigated. The simulation results show that the estimated secret key rate without our proposed scheme is about 10.7 times higher than the realistic rate at 18 km transmission distance when the variance of RIN is only 0.4. What's worse, the difference becomes greater and greater with the increase of the variance of RIN. Thus, our proposed scheme makes sense in further completing the practical security of CV-MDI QKD system. In other words, our work enables CV-MDI QKD system not only to resist all attacks against detectors, but also to close the vulnerability caused by the actual source, thus making the scheme closer to practical security.