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 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.