Through silicon via （TSV） technology refers to the silicon micro-hole processing technology used to achieve vertical conduction and interconnection between chips. The three-dimensional （3D） morphology of TSV samples is commonly measured using destructive scanning electron microscope （SEM） profile imaging technology. In addition， white light interference technology has the advantage of non-destructive measurement； however， it is difficult to probe the light reaching the bottom of TSV samples with an aspect ratio higher than 6：1， and the topography is also distorted. To address this problem， a near-infrared micro-interference detection method based on aberration compensation is proposed in this paper. The method uses near-infrared broadband light as the probe light source， which can penetrate through the TSV. Moreover， an adaptive aberration compensation module in the form of a deformable mirror is introduced into the detection system to compensate for the modulation aberration that is synchronously generated by the TSV. The first step of detecting the TSV 3D topography is to set the type and quantity of the aberration that needs to be compensated by the deformable mirror. This is obtained using the finite element simulation software COMSOL Multiphysics based on the aberration modulation law for a 3D TSV high aspect ratio structure under the probe light. Subsequently， the evaluation function index threshold based on the frequency domain is used to estimate the focus state of the TSV bottom image. Furthermore， the refocusing ability of the probe light is essentially improved and a clear bottom image of the tested TSV is obtained. On this basis， the depth value of the tested TSV and its 3D topography distribution is calculated using vertical scanning interferometry. Finally， two types of TSV samples with a diameter of 10 μm and depth of 65 μm （aspect ratio 6.5）， and diameter of 10 μm and depth of 103 μm （aspect ratio 10.3）， are measured using the proposed method. The results show that the relative error of depth measurement is 1% compared with that of the high-precision SEM measurement results. Moreover， the proposed method can obtain a clear image of the TSV bottom with a high aspect ratio， and can also effectively enhance the wide spectrum interference signal and fringe contrast at the bottom compared with white light microscopic interference. Therefore， the proposed method can be used to precisely measure the 3D topography of TSVs with a higher aspect ratio.