Disclosed is an apparatus and method of processing input and output in a multi-kernel system. A method of processing input and output in a multi-kernel system according to the present disclosure includes: setting a shared memory between a first kernel on a main processor and a lightweight kernel on a parallel processor; setting a data transmission and reception channel between the first kernel on the main processor and the lightweight kernel on the parallel processor using the shared memory; providing, on the basis of the data transmission and reception channel, an input/output task that occurs in the lightweight kernel to the first kernel on the main processor; processing, by the first kernel on the main processor, an operation corresponding to the input/output task; and providing a result of the processing to the lightweight kernel.