The mechanism design theory can be applied not only in the economy but also in many fields, such as politics and military affairs, which has important practical and strategic significance for countries in the period of system innovation and transformation. As Nobel Laureate Paul said, the complexity of the real economy makes it difficult for “Unorganized Markets” to ensure supply-demand balance and the efficient allocation of resources. When traditional economic theory cannot explain and calculate the complex scenes of reality, we require a high-performance computing solution based on traditional theory to evaluate the mechanisms, meanwhile, get better social welfare. The mechanism design theory is undoubtedly the best option. Different from other existing works, which are based on the theoretical exploration of optimal solutions or single perspective analysis of scenarios, this paper focuses on the more real and complex markets. It explores to discover the common difficulties and feasible solutions for the applications. Firstly, we review the history of traditional mechanism design and algorithm mechanism design. Subsequently, we present the main challenges in designing the actual data-driven market mechanisms, including the inherent challenges in the mechanism design theory, the challenges brought by new markets and the common challenges faced by both. In addition, we also comb and discuss theoretical support and computer-aided methods in detail. This paper guides cross-disciplinary researchers who wish to explore the resource allocation problem in real markets for the first time and offers a different perspective for researchers struggling to solve complex social problems. Finally, we discuss and propose new ideas and look to the future.