We present an isogeometric thin shell formulation for multi-patches based on rational splines over hierarchical T-meshes (RHT-splines). Nitsche’s method is employed to efficiently couple the patches. The RHT-splines have the advantages of allowing a computationally feasible local refinement, are free from linear dependence, possess high-order continuity and satisfy the partition of unity and non-negativity. In addition, the C1 continuity of the RHT-splines avoids the rotational degrees of freedom. The good performance of the present method is demonstrated by a number of numerical examples. •We present a multi-patch isogeometric large deformation thin shell formulation based on RTH splines. It is an extension of our previous work on RHT-spline shells to large deformations and multiple patches. The coupling is based on Nitsche’s method and allows also coupling of a shell to a solid model.•Furthermore, we present a stress recovery technique to drive the adaptive h-refinement procedure in isogeometric thin structures.•The method is validated for several linear and non-linear benchmark problems including the pinched cylinder and hemispherical shell, a wind turbine rotor accounting for large deformations, a hemispherical shell with a stiffener and a pinched cylinder considering large deformations.