A manufacturing method of common mode filters and a structure of the same are revealed. A common mode choke layer is disposed over a composite substrate and a second magnetic material layer is coated on an upper surface of the common mode choke layer. The common mode choke layer is produced by a wafer-level electrode leading out method and having leading-out terminals on sides thereof. External electrodes are formed on sides of the common mode choke layer by partial cutting, sputtering, lithography and electroplating at wafer level and corresponding to the leading-out terminals. Thereby common mode filters produced are supported more stably. Moreover, the volume is minimized due to inductive coils and external electrodes connected by wafer level packaging. Thus the common mode filters are mass-produced, the cost is down and the defect rate is reduced.