With the complexity and volume of onboard software increasing, on-orbit refactor for software update and maintenance comes more important. As the software scale becomes larger, it is too hard to refactor software by low-speed channel in one observation arc. At the same time, large software makes data storage space more scarce, and traditional methods such as triple-mode redundancy cannot be used to ensure the reliability and security of program data. Therefore, a reliable refactor scheme for large-scale onboard software by using high-speed channel is proposed. Let the boot loader which store in read-only PROM be the fundamental guarantee of this scheme. A safe mode program saved in MRAM which is used to refactor the onboard software by high-speed channel is the kernel of this scheme. Meanwhile, adding a self-refactor function in onboard software as the most commonly used refactor method. The ground tests and on-orbit experiments indicated that this scheme can refactor large software with high speed and high reliability, which means it can update and maintain the onboard software safer and more convenient.