Low-coherence vertical scanning interferometry is an effective method for non-destructive testing of micro-structure topography characteristic parameters. However, when the groove aspect ratio of the microstructure is higher than 5∶1, the shading effect and the complex diffraction effect of the step edge will lead to an abnormal vertical scanning measurement interference signal which should contain only one envelope, forming two or even more envelopes, which in turn affects the topography detection results. Establishing an accurate model to describe the modulation of the detection signal by the measurement system and the tested micro-structure parameters is the basis for analyzing the formation mechanism and law of abnormal interference signals, and proposing corresponding topography recovery algorithm. However, the multiple scattering of probe light by the high aspect ratio trench structure is very complicated, and the current diffraction theory is difficult to describe perfectly. The finite difference time domain method can accurately simulate the transmission process of the light field in a discrete time progressive sequence by numerically solving the Maxwell difference equations of the probe light field interacting with the micro-structures. In this paper, the measurement process of low-coherence vertical scanning interferometry is analyzed, and the finite difference time domain method is used to numerically simulate the microscopic imaging and coherent scanning measurement process of the low-coherence microscopic interferometry system, and calculate the modulated light field on the surface of the tested micro-structures and the interference field on the image plane, and finally a low-coherence microscopic interference signal is obtained. The interference signals of the Si-based trench micro-structures with aspect ratios of 5∶1 and 80∶3 are simulated respectively, and compared with the experimental signals of the trench microstructures with above-mentioned aspect ratio measured by the self-developed Linnik type low-coherence vertical scanning interference system. By comparison, the double-envelope characteristics and double-peak characteristics in frequency distribution of the interference signal of the high aspect ratio trench structure are matched to verify the accuracy of the proposed simulation method. The simulation method can be applied to a priori simulation calculation of the low-coherence microscopic interference signal of the measured structure before the actual measurement. By analyzing the signal characteristics in advance, it can guide the optimization direction for the selection and improvement of the topography restoration algorithm.