Different from the organization structure of complex projects in Western countries, the Liang Zong hierarchical organization structure of complex projects in China has two different chains, the chief-engineer chain and the general-director chain, to handle the trade-off between technical and management decisions. However, previous works on organization search have mainly focused on the single-chain hierarchical organization in which all decisions are regarded as homogeneous. The heterogeneity and the interdependency between technical decisions and management decisions have been neglected. A two-chain hierarchical organization structure mapped from a real complex project is constructed. Then, a discrete decision model for a Liang Zong two-chain hierarchical organization in an NK model framework is proposed. This model proves that this kind of organization structure can reduce the search space by a large amount and that the search process should reach a final stable state more quickly. For a more complicated decision mechanism, a multi-agent simulation based on the above NK model is used to explore the effect of the two-chain organization structure on the speed, stability, and performance of the search process. The results provide three insights into how, compared with the single-chain hierarchical organization, the two-chain organization can improve the search process: it can reduce the number of iterations efficiently; the search is more stable because the search space is a smoother hill-like fitness landscape; in general, the search performance can be improved. However, when the organization structure is very complicated, the performance of a two-chain organization is inferior to that of a single-chain organization. These findings about the efficiency of the unique Chinese-style organization structure can be used to guide organization design for complex projects.