This paper introduces a novel lightweight clock synchronization protocol (LCSP) and BUB clock synchronization algorithm based on real-time micro-kernel. Unlike other clock synchronization approaches which rely on redundant exchanged messages, this approach takes advantages of the traffic smoothing technique at each end node to suppress or "block" other traffics during the clock synchronization duration. The BUB algorithm efficiently decreases the number of synchronization messages exchanged during each synchronization round and can easily extend to large distributed real-time systems. Performance evaluation results prove that the LCSP protocol and the BUB algorithm can provide perfect synchronization precision and are appropriate for most distributed hard real-time and embedded control systems, when integrated with the traffic smoothing technique.