AbstractAdvanced intersection control systems have been created to alleviate traffic congestion. CAVs may benefit from cooperative navigation in order to address the regular traffic issue. Due to whole uncertainty in transportation network, the conventional motion planning for local areas may lead to undesirable effects in long run. In prior works, a micro–macro flow control (MiMaFC) strategy is used to investigate CAVs' navigation at unsignalised intersections by taking flow velocity and vehicle passing priority into account. To get a better understanding of motion control and how it can be utilised to impact traffic flow behaviour, this study expands the intersection navigation protocol and develops a velocity planning methodology based on the proposed MiMaFC technology. Correspondingly, cooperative navigation protocol used in the addressed architecture is specifically developed for CAVs that continually cross intersections. Further, spatio‐temporal velocity adaption mechanism is presented in this work. Depending on the vehicles' location and speed, CAVs might use either the MiMaFC‐based or self‐interested velocity strategy. Simulation results, which include a congested traffic network, are shown to demonstrate the proposed method's potential. The study found that the suggested motion planning framework may increase urban network mobility over a non‐supervised CAVs system.