The spacecraft relative motion trajectory planning is one of the enabling techniques for autonomous proximity operations, especially in the increasingly complicated mission environments. Most traditional trajectory planning methods focus on improving the performance criteria in the deterministic conditions, whereas various uncertain elements in practice would significantly degrade the trajectory performance. Considering the uncertainties underlying the collision avoidance constraints, this paper suggests a model predictive control based online trajectory planning framework in which the obstacle information in higher-precision would be consistently updated by the onboard sensor. To improve the computational efficiency of the online planning framework, the rotating hyperplane (RH) technique is utilized to transform the nonlinear ellipsoidal keep-out zone constraints into convex formulations. And the concept of rotation window is introduced to eliminate the unexpected mismatch between the spacecraft motion and hyperplane rotation in the conventional RH method, which in sequence improves the RH method’s capability for multiple obstacle avoidance problem. Moreover, a three-dimensional (3-D) extension strategy is proposed to simplify the computation procedure when applying the RH method for a 3-D collision avoidance problem. Numerical simulations are carried out to validate the performance of the proposed online trajectory planning framework in addressing the uncertain collision avoidance constraints.