Sharding is a key technology to improve the scalability of blockchain, and cross-shard transaction protocols are the core of sharding to ensure transaction atomicity and consistency. Many scholars have conducted related research, including two-phase commit (2PC), transaction splitting, relay transactions, and deterministic ordering. However, there remains a challenge in balancing the efficiency and atomicity of cross-shard transactions (CTXs). Thus, this paper proposes a parallel and atomicity-guaranteed cross-shard transaction protocol, BMDS-Shard. Firstly, by decoupling cross-shard transactions into synchronized transactions in the source and target shards through beacon nodes, and automatically identifying cross-shard processing flows, we assign higher processing priority within shards, thereby solving the inefficiency of relay transactions. Secondly, based on a multi-beacon node data snapshot mechanism, we ensure instant and reliable state data feedback to the source shard, addressing the insufficient atomicity of transaction splitting. Finally, we have implemented the BMDS-Shard protocol, conducted theoretical analysis, and performed experimental validation on the BlockEmulator platform. Both theoretical and experimental results demonstrate that while guaranteeing transaction atomicity, our protocol reduces cross-shard transaction confirmation latency by 65.82% and 65.06% compared to existing relay transaction protocols Monoxide and BrokerChain, respectively.