The invention discloses a method and a system for manufacturing a multi-gate transistor to improve the performance of the multi-gate transistor. Each gate of the transistor is provided with a gate dielectric layer correspondingly. The method comprises the following steps that: when a plurality of removing processes capable of removing the same matters to be removed are provided between the manufacture of the current gate dielectric layer and the manufacture of the next gate dielectric layer, part removing processes of the plurality of removing processes are adopted to remove the matters to beremoved; and in the plurality of removing processes, the influence of other removing processes except for the part removing processes on the implementation effect of the respective subsequent processcan be ignored.