A computer input system and an input method thereof are disclosed. The computer input system includes a storage unit, a representative number obtaining module and a coding module. The storage unit stores four carry radices, and the four carry radix have one-to-one correspondences to an amount of initial consonants, an amount of head vowels, an amount of vowels and an amount of tones of a phonetic notation symbol, respectively. After the representative number obtaining module obtains four symbol representative numbers according to a Chinese character phonetic notation, the coding module generates a coding number of the Chinese character according to the symbol permutation order, the four carry radices and the four symbol representative numbers.