The transparent windshield is a key structural part of the aircraft, which requires outstanding performance. To reduce weight, the aircraft′s transparent windshield utilizes a heterogeneous multi-layer composite structure of “organic glass-transparent polycarbonate-organic glass”, where the performance is closely related to the thickness of each layer of the transparent windshield. Existing measurement methods cannot meet the comprehensive requirements for efficient and high-precision layer-by-layer thickness measurement of the transparent windshield. Therefore, a new method for spectral-domain low-coherence measurement of the multi-layer transparent windshield is proposed. Firstly, by using the orthogonal dispersion to enhance dispersion capability, the measurement range is increased. Then, a mapping model between the thickness of the transparent windshield and the spectral wavenumber is formulated, and the model parameters are calibrated with high-precision parallel flat crystal. Finally, a measurement system is established. Experimental results show that the proposed method has a maximum range exceeding 41 mm, with micrometer-level measurement accuracy, and a measurement speed less than 8 ms. It can meet the requirements for thickness measurement of the multilayer aircraft transparent windshield.