The MW high-voltage power system is the key device in the field of particle accelerators, and its reliability is a critical performance indicator. The fault of the submodule (single TLB) in the multi-parallel three-level boost (TLB) converter will affect the reliable operation of the MW high-voltage power system. In order to solve this problem and improve the reliability of the system, a fault-tolerant control strategy based on voltage-current double closed-loop control and capacitor voltage balance control is proposed in this paper. Specifically, a general AC small-signal model for the multi-parallel TLB converter is first developed by using the state-space averaging method. Then, based on the model, a controller is designed for a kilovolt multi-parallel TLB converter (taking 1.2 kV triple as an example). The control loops are coupled to make the output voltage stable and the capacitor voltage remains balanced. Sufficient experiments verify that the proposed fault-tolerant control strategy can make the triple-parallel TLB converter operate fault-tolerant when the submodules are removed due to faults, resulting in a highly reliable and fault-tolerant system.