The invention discloses a method and system for detecting a transformer winding based on modal analysis, and the method comprises the steps: carrying out the modal analysis of a to-be-detected transformer winding segment, and determining the inherent frequency of the to-be-detected transformer winding under different order vibration modes; when the natural frequencies are not in the preset range,determining that the transformer winding to be tested is qualified. According to the invention, segmented modal analysis is carried out on the transformer winding model to obtain the inherent frequency of the transformer winding under different order vibration modes, and the transformer winding is detected according to the inherent frequency; meanwhile, the pre-tightening force is applied in the modal analysis process to simulate the actual operation condition, so that the analysis result is more accurate; the analysis result can comprehensively check whether the inherent frequency of the transformer winding has power frequency or frequency multiplication, resonance of the transformer winding can be avoided, and a basis is provided for checking the anti-short-circuit capability of the transformer winding.