The invention provides a method for controlling torsion of a base isolation structure. A displacement ratio, a ratio of a torsion component to a translational motion component and a torsion shearing force ratio are taken as torsional effect indexes, torsional effect index values are acquired and adjusted to accord with limit values, and accordingly, torsion of the base isolation structure of a complicated and irregular system is controlled. The method specifically comprises steps as follows: a three-dimensional finite element model of an irregular to-be-isolated system is established, isolation support parameters are determined in combination of a limiting value of the offset distance between the center of rigidity and the center of mass of an isolation layer, an isolation structure model is established, the torsional effect index values are extracted, whether the torsional effect index values meet the requirements of limit values is judged, a corresponding technical route is adopted according to the ultralimit condition, and finally, the torsional effect index values can all meet the requirements. According to the method, as for the complicated and irregular isolation structure, an effective torsion effect index and a specific implementation method are provided quantitatively, quantitative standards and specific operation standards are provided for an isolation technology for controlling torsion of the structure, and larger application and promotion values are provided.