Digital twin (DT) technology plays a fundamental role in innovation in the energy field. At present, research of nuclear reactor DT is mainly focused on methodologies of multi-disciplinary, multi-physical, and multi-scale coupling simulation. However, the lack of research on multi-probability seems to limit the DT application. Multi-probabilities are widely found in reactor operation, such as process measurement uncertainty, equipment degradation uncertainty, theoretical model uncertainty, and so on. How to realize the DT of the reactor system based on the multi-probability principle to achieve the real-time operation state and the remaining useful life estimation, and to realize the autonomous operation control under the uncertainties, are the current hotspot and difficult issues. The solutions of a reactor core DT platform HeTu are discussed in this paper for probability estimation and probability control based on probability programming methodologies. The results show that Bayesian estimation and model prediction control methods proposed in HeTu could obtain satisfactory results for practical application.