A phrase input system and a method thereof that is applicable for a handwriting input apparatus is disclosed. The phrase input system comprises a database, an input unit, an output unit, an identification unit, and a comparison unit. The database stores a collection of phrases. The input unit is used for inputting a handwriting phrase that includes at least one handwriting character. The identification unit identifies the handwriting phrase to produce an effective phrase. The comparison unit compares the effective phrase and the collection of phrases in the database in order to find an optimum phrase. The optimum phrase is displayed through the output unit. When the phrase input system is applied to the handwriting input apparatus, the recognition rate of the handwriting is improved.