The benefits of higher data transmission rates, extensive communication frequency bandwidths, reduced power consumption, and enhanced anti-interference capabilities make inter-satellite optical communication (ISOC) a promising technology for the future. However, during orbital motion, satellites are subjected to external perturbation forces, which affect the performance of the ISOC system. This paper establishes an ISOC system consisting of two co-orbital satellites orbiting the Earth under the influence of perturbations. For what we believe to be the first time, the probability density function (PDF) of the radial displacement caused by perturbations is introduced. Subsequently, a PDF detailing the inter-satellite pointing errors, while accounting for the effects of perturbations and platform vibrations, is presented. Moreover, pointing errors and plasma absorption are considered in the PDF derivation process for the end-to-end ISOC system. The closed-form expression for the average bit-error rate (BER) of the proposed system is derived using Meijer’s G function. Simulation results are provided to validate the theoretical expression. The findings show that key parameters associated with perturbations significantly influence the PDF of inter-satellite pointing errors and the average BER of the proposed ISOC system.