Abstract It is well-known that three-family supersymmetric Pati–Salam models from intersecting D6-branes, where either one or both of the $$\textrm{U}(2)$$ U ( 2 ) gauge factors are replaced by a $$\textrm{USp}(2)$$ USp ( 2 ) group, are quite scarce. In order to construct all such kind of models with generic additional gauge symmetries, we fix the observable sectors and study all the possible hidden sectors. Thus, we are able to completely determine all types of such kind of the inequivalent models on a $$\mathbb {T}^6/(\mathbb {Z}_2\times \mathbb {Z}_2)$$ T 6 / ( Z 2 × Z 2 ) orientifold from IIA string theory. We find the gauge coupling relations to be highly sensitive to the variations in the hidden sector. One of the models exhibits the gauge coupling unification for a particular solution at the string scale. In addition, we perform scan on the hidden sector variations for the models presented in arXiv:2112.09632 , whose gauge coupling relations are still preserved. Thus, we fix the gap in the previous study and complete the model building for all the inequivalent models.