Abstract The multipartite unitary gates are called genuine if they are not product unitary operators across any bipartition. We mainly investigate the classification of genuine multipartite unitary gates of Schmidt rank two (SR-2), by focusing on the multiqubit scenario. For genuine multipartite (excluding bipartite) unitary gates of SR-2, there is an essential fact that their Schmidt decompositions are unique. Based on this fact, we propose a key notion named as singular number (SN) to classify the unitary gates concerned. The SN is defined as the number of local singular operators in the Schmidt decomposition. We then determine the accurate range of SN. For each SN, we formulate the parametric Schmidt decompositions of genuine multiqubit unitary gates under local equivalence. Finally, we extend the study to three-qubit diagonal unitary gates due to the close relation between diagonal unitary gates and SR-2 unitaries. We start with discussing two typical examples of SR-2, one of which is a fundamental three-qubit unitary gate, i.e. the CCZ gate. Then we characterize the diagonal unitary gates of SR greater than two. We show that a three-qubit diagonal unitary gate has SR at most three, and present a necessary and sufficient condition for such a unitary gate of SR-3. This completes the characterization of all genuine three-qubit diagonal unitary gates.