Recently, with the increasing demand for high-accuracy three-dimensional (3D) imaging and localizing of the internal subcellular structures in cells, quantitative refractive index tomography technique has been developed and widely applied in various fields, such as molecular biology, biochemistry and cell biology. Thanks to the noninterference, large field of view and high resolution advantages of traditional Fourier ptychographic microscopy (FPM) technique, quantitative phase tomography (QPT) method based on multi-slice (MS) FPM has attracted considerable attention lately. However, since the reported MS model is simply established on the traditional two-dimensional FPM, it is difficult to characterize the 3D diffractive propagation properties under large oblique illumination angles accurately. In order to solve this problem, an improved MS model for 3D FPM is proposed in this paper. First, the phase difference image of each slice under the vertical illumination is regarded as the standard phase map. Then, based on the law of refraction, the true phase delay of each slice under large oblique illumination angle is established according to the 3D optical path difference variation. The numerical error between the true phase delay and the standard phase map is then compensated in the iterative reconstruction algorithm, and finally the reconstruction accuracy and quality of the 3D QPT could be improved.