Research on the ecosystem service effects of land use change in complex ecosystem can provide an important basis for optimizing land spatial pattern and strengthening ecosystem management. Taking Zhangye City, a typical area of Mountain-Oasis-Desert complex system in arid area as an example, based on three phases of land use data in 1987, 2000 and 2018, taking the township administrative region as the basic unit, the comparative advantage index is introduced to divide the mountain, oasis and desert sub-system, and the land use change characteristics of the complex system and the trade-off/synergy effects of ecosystem services are studied. The results show that:(1) The complex system of Zhangye City presents the characteristics of regional differentiation, which is composed of southern mountain system, central oasis system and northern desert system. The mountain system is mainly consisted of forest land and grassland, the oasis system is mainly consisted of cultivated land and construction land, and the desert system is mainly consisted of unused land. (2) In terms of time change, the land use change of each system was more intense from 2000 to 2018. Among them, the increase of the cultivated land area of oasis system was the largest with 363.08 km², and the increase rang of the construction land area of desert system was the largest with 78.23%. The land use transfer mode of each system is as follows:the mountain system is mainly from grassland turn into cultivated land, and the oasis system and desert system are mainly from unused land turn into cultivated land. (3) The ecosystem service value of the complex system in Zhangye City shows an increasing trend. Among them, the increase rang of the ecosystem service value of the desert system is the largest. The relationship between the value of each sub-system is mountain system > oasis system > desert system, and compared with other land use types, the contribution of the cultivated land to the ecological service value of each system is the largest. (4) The synergy effect of land use change in Zhangye is greater than the trade-off effect. Among them, the ecosystem services of the desert ecosystem are all synergistic relationships. The supply service of the mountain system has a trade-off relationship with other services, accounting for 32.73% of the trade-off relationship, and the regulation service of the oasis system has a trade-off relationship with other services, accounting for 18.18% of the trade-off relationship.