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The dual-core environment is more and more popular in embedded system recently. The limited buffer and limited bandwidth are critical for parallel algorithm in embedded system. This paper proposes a novel parallel algorithm using functional partitioning with dynamic load balance for video decoder. The video decoding flow of each macroblock is dynamically separated for different cores according to the buffer queue level. The extra intercommunication buffer size requires only 1.6% buffer size of traditional data partitioning algorithm for 720p decoder. The speed-up ratio is 1.74 times in average compared to original single thread code. The experiment result shows the proposed algorithm can real-time decode H.264 720p high profile on ARM Cortex-A9 400MHz dual-core system.