A new multiscale computational method, named the 3D extended multiscale finite element method (3D-EMsFEM), is established for the mechanical analysis of 3D nastic structures composed periodically of embedded microcapsules. Accordingly, a type of more reasonable boundary conditions, i.e. periodic boundary conditions, is introduced to construct the numerical base functions for the 3D-EMsFEM. To improve the accuracy, a high order coarse-grid element is developed, which is expected to work better than that with the conventional coarse-grid element to calculate the small-scale information in the nastic structures. Furthermore, a coupled EMsFEM (CEMsFEM) is proposed for the active response prediction of 3D nastic structures with consideration of the ion transport in the active membrane. Numerical results are given and indicate that the method developed can be efficiently used for the numerical analysis of the active response of 3D nastic structures.