The operation of multi‐agent systems (MAS) in space necessitates considerations for obstacle avoidance, collision prevention, and connectivity among agents. This coupling conflict, stemming from spatial resource utilization, poses a significant and non‐negligible threat to the safe operation of MAS. This article proposes a consensus control scheme for the time‐varying formation of MAS, incorporating functions for maintaining connectivity, collision avoidance, and obstacle dodging. This scheme effectively constrains the time‐varying formation tracking error within an arbitrarily small range. The considered system model takes a high‐order nonlinear form, with uncertainties and disturbances present in each order. This grants the control scheme with high generality and practicability. By employing barrier Lyapunov function to delineate the safe operational space of MAS, conflicts in spatial resource utilization are avoided. This approach simultaneously fulfills the requirements for connectivity maintenance, collision avoidance, and obstacle dodging in the safe operation of MAS. An additional rotation operator is integrated into the controller to smoothly address the “minima” problem, eliminating the need for external intervention. Gaussian radial basis function is used to estimate the nonlinear terms, uncertainties, and unknown perturbation online in the system. The stability of the MAS under the proposed control scheme is analyzed through Lyapunov function. Finally, numerical simulation results are demonstrated to explain the effectiveness of the control scheme.