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A modified random fiber removal algorithm is proposed to numerically study transverse elastic properties of unidirectional carbon fiber reinforced pyrolytic carbon (C/C) composites. This method can efficiently generate the Representative Volume Element (RVE) of composites with random distribution fibers. On the basis of the numerical homogenization strategy, the effect of interphase between carbon fiber and pyrolytic carbon on the mechanical behaviors of unidirectional C/C composites are investigated. Meanwhile, periodic boundary conditions and linear elastic constitutive materials are taken into account. For validation, numerical calculations are compared with these obtained by atomic force microscopy (AFM) tests, which shows that more accurate results will be pursued when the interphases are considered. In addition, the influences of interphase parameters including the thickness, modulus, and Poisson’s ratio, on the effective transverse behavior of unidirectional C/C composites are studied numerically.The results demonstrate that the effective transverse properties of unidirectional C/C composites are mainly determined by the interphase modulus and independent of the interphase Poisson’s ratio. If the interphase thickness (less than 140 nm) of unidirectional C/C composites are very small, the modulus of interphase beyond 8 GPa makes little effect on the effective transverse properties.