The invention provides an embedded circuit flexible circuit board and a preparation method thereof. The preparation method of the embedded circuit flexible circuit board comprises the following steps:providing a first substrate, wherein the surface of the first substrate is attached with a flexible material layer, and the flexible material layer has convex structures; forming a second substrate on the surface of the flexible material layer, so that groove structures adapted to fit the convex structures are formed on the surface of the second substrate; and forming a conductive circuit in thegroove structures after the second substrate is stripped. Through the embedded circuit flexible circuit board and the preparation method thereof provided by the invention, the problem in the prior artthat the embedded circuit can not be prepared on the flexible substrate by means of the FPC preparation technology is solved.