In this letter, in this process of using matrix pencil method (MPM) to perform the equivalent of the multiport frequency‐dependent system, a modified MPM is proposed to realize the solutions of common poles and residue matrix in time domain. In this technique, the frequency domain data of all ports are transformed into the time domain matrix vectors by IFFT. Then, the time domain matrix vectors are superimposed into a single vector, which is analyzed by the MPM to generate a common set of poles. The residue matrix is obtained by using the least square method to solve the equation consisting of the common poles and the time domain matrix vectors. The fast evaluation of the frequency domain data of the multiport frequency‐dependent system can be thus completed by the common poles and residue matrix. Finally, the correctness of the proposed method is verified by a three‐conductor transmission lines system.