The present invention provides a fin-shaped field effect transistor (FinFET), comprises: a substrate having a fin structure; a plurality trenches formed on the fin structure with an alloy grown in the trenches; a gate structure on the fin structure perpendicular to an extending direction of the fin structure in-between the plurality of trenches; and an amorphous layer on a surface of the fin structure exposed by the gate structure and disposed in-between the gate structure and the alloy. The invention also provides a manufacturing method of a fin-shaped field effect transistor (FinFET).