In recent years, underground logistics systems have attracted more and more attention from scholars and are considered to be a promising new green and intelligent transportation mode. This paper proposes a yard design problem considering an underground container logistics system. The structure and workflow of the underground container logistics system are analyzed, and key features are recognized for the yard design problem, such as the container block layout direction, the lane configuration in the yard, and the number of container blocks. We formulate the problem into mathematical models under different scenarios of the key features with the comprehensive objective of maximizing the total throughput and minimizing the total operation cost simultaneously. An improved tabu search algorithm is designed to solve the problem. Experimental results show that the proposed algorithm can generate a satisfactory layout design solution for a real-size instance. Our research studies different container yard design options for introducing the underground logistics system into port terminals, which provides an important scientific foundation for promoting the application of underground container logistics systems.