The invention provides a method for determining the size of a sub model in structure multi-scale dynamic analysis. The method solves the problem that in large-structure multi-scale dynamic analysis, the size of the sub model is difficult to accurately determine. According to the method, firstly, a whole model of a large structure is built, key portions of the structure are determined according to overall analysis results, and an initial sub model is built; dynamic response calculation is carried out on the initial sub model, and the result is beta 1; the size of the initial sub model is increased by a times, an updated sub model is built, and the dynamic response result of the updated sub model is beta 2; the assurance rate delta for analyzing result accuracy is calculated according to beta 1 and beta 2, and whether the calculation result accuracy meets requirements and whether the size of the sub model needs to be increased are determined according to the comparison of the delta and the set optimal assurance rate. The problem that modeling analysis of a whole large complicated structure wastes machines and time is avoided, modeling and calculation efficiency of structure multi-scale dynamic analysis is improved, accuracy and reliability of the calculation result are guaranteed, and the method is convenient to popularize and use among analyzers working on construction design.