Different industrial applications essentially require a reliable communication without data loss for smooth functioning and better control performance. Controller Area Network (CAN) bus based Distributed embedded systems can provide better communication solution to satisfy this requirement. In addition to this, also provides safety for critical applications, inter-operability between systems, data sharing applications, etc…. with cost effectiveness. In a Digital Data communication, Clock synchronization is important for data quality and security. For CAN bus, different methods of clock synchronization mechanism for noise reduction were developed earlier. In this paper we propose and implement a new mechanism of "Multi-coded EX-OR Masking technique" to reduce jitter-noise and drift during trans-receiving a long sequence of identical bits.