The expansion project of Terminal 3 at Lijiang Sanyi International Airport has posed numerous challenges for the structural design due to site constraints and the unique shape of the roof structure. First, the site is located in a high seismic intensity zone (8 degrees, 0.3g) and lies relatively close to a fault zone, making seismic resistance challenging for the structure. Meanwhile, due to the steep slope within the site, excavation in elevated areas and backfilling in lower areas have increased the difficulty of foundation design. Additionally, the roof’s multiple continuous side skylights results in poor structural integrity. The use of basic friction pendulum isolation technology in the central area reduces seismic forces by nearly 70%, significantly lowering seismic energy input and improving the structure’s overall seismic performance. Roof damping technology is applied in the finger gallery area to improve the seismic ductility of single-span structures. To address uneven foundation conditions, a combination of long and short piles with variable leveling design is adopted. Finite element numerical analysis shows that the maximum settlement value is 35 mm, and the differential settlement is 0.47%L(L is the span of base). A roof solution using cross-type three-dimensional trusses combined with plane trusses is adopted to meet the load-bearing requirements while better adapting to the building’s shape and functional requirements.