The wing root joint area for civil aircraft is the critical area where the accumulated load from wing and fuselage is balanced and exchanged. There are extremely high design requirements and constrains for its design considering the structure safety, durability, efficiency and assembly coordination, as well as the detail design. This article presented the difficulties of the typical root joint of civil aircraft, specific load transition requirements, the root rib layout principle, key characteristics and comparison analysis of different main root joint concept. Based on the requirements, an optimized design philosophy for compliance compensation and assembly stress relaxation was presented, which had been validated to be feasible by test results. The key points of composite wing root joint design were discussed considering the composite mechanical characters and the corresponding proposal was provided.