With the rapid development of high-throughput experiments, detecting functional modules has become increasingly important in analyzing biological networks. However, the growing size and complexity of these networks preclude structural breaking in terms of simplest units. We propose a novel graph theoretic decomposition scheme combined with dynamics consideration for probing the architecture of complex biological networks.Our approach allows us to identify two structurally important components: the "minimal production unit"(MPU) which responds quickly and robustly to external signals, and the feedback controllers which adjust the output of the MPU to desired values usually at a larger time scale. The successful application of our technique to several of the most common cell regulation networks indicates that such architectural feature could be universal. Detailed illustration and discussion are made to explain the network structures and how they are tied to biological functions.The proposed scheme may be potentially applied to various large-scale cell regulation networks to identify functional modules that play essential roles and thus provide handles for analyzing and understanding cell activity from basic biochemical processes.