A multi-functional composite substrate structure is provided. The first substrate with high dielectric constant and the second substrate with low dielectric constant and low loss tangent are interlaced above the third substrate. One or more permeance blocks may be formed above each substrate, so that one or more inductors may be fabricated thereon. One or more capacitors may be fabricated on the first substrate. Also, one or more signal transmission traces of the system impedance are formed on the second substrate of the outside layer. Therefore, the inductance of the inductor(s) is effectively enhanced. Moreover, the area of built-in components is reduced. Furthermore, it has shorter delay time, smaller dielectric loss, and better return loss for the transmission of high speed and high frequency signal.