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By combining the mode matching (MM) technique and the finite-difference frequency-domain (FDFD) method, a hybrid method is proposed for computing frequency responses of waveguides with multiple discontinuities. In the method, the computational domain is divided into subdomains, and the final matrix equation is a Schur complement system. In the numerical examples, the method is compared to the classical finite-difference frequency-domain method and the partial eigenfunction expansion finite-difference frequency-domain method. The results show that this method is more efficient and accurate than the others.