An electronic module having an electromagnetic shielding structure and its manufacturing method are provided. At first, a first substrate and a second substrate are separately provided. At least one electronic element and at least one connection pad are formed on a surface of the first substrate. The second substrate includes a conductive film and at least one conductive bump is formed on a surface of the conductive film. The first substrate and the second substrate are laminated together wherein the conductive bump is aligned with and connected to the connection pad to obtain the electronic module.