The CO2 transcritical Rankine cycle (CO2-TRC) has a great potential for the application in concentrating solar power (CSP) system due to the advantages of using low- and medium- temperature sources and compact structures. However, the cloud passages always lead to the suddenly varied heat input to the system, while understanding the system’s response to the cloud disturbance may enable the operational stability which is viable for driving the advanced CO2-TRC system. In this study, a dynamic thermodynamics model is developed to simulate the response behaviors of the simple and regenerative CO2-TRC based trough CSP systems under various cloud disturbances. The results show that by examining the system’s performances, the cloud thickness mainly affects the variation range, while the cloud cover duration mainly affects recovery time. At the same cloud thickness, the recovery time for the regenerative system could be about three times longer than that for the simple system. Subject to the cloud with same cover duration, the simple system tends to reach the stable state in the shorter time. As the collector is shaded by a moving cloud, the system’s recovery time is almost same but the system efficiency has the smaller decrease as compared to the stationary cloud coverage with the same duration. These results allow determining the optimal design and operating scheme of the CO2-TRC based CSP systems to increase the output power and operating stability.