The mathematical control model for dynamic start-up process of the VTE-MED seawater desalination system was establishedemploying the previous developed non-linear differential equations for system design and performance analysis. The influences on thestart-up process of the operating parameters, such as the initial feed brine flow rate and the top brine temperature were analyzed.The relationships among the feed brine flow rate, the gained output ratio (GOR) and the start-up time were also investigated, whichcan be evidence to determine the optimal initial feed brine flow rate. The results also indicate that the system can consume the total heatrating generated by the low temperature nuclear heating reactor (LT-NHR) even at the most initial start-up stage, implying the presentdesalination system has excellent coupling characteristics with the LT-NHR. With necessary experiments verifications, the start-up controlmodel developed in this paper can be the theoretical base for the analysis of dynamic performances of the seawater desalinationsystem.