Fuyuan City is located in the black soil region of northeast China. Its fertile soil and flat terrain provide a reliable guarantee for the scale, intensification, and standardization of farmland. A large amount of land resources that can be used for the national food base has been developed, and the contradiction between the need for wetland protection and arable land development has become increasingly prominent. Based on the remote sensing data of 2000, 2005, and 2010, this paper simulates the future land use/land cover changes structure in Fuyuan City based on the Markov Chain model. According to the characteristics of Fuyuan City’s structure, economy, society, and natural environment, within the overall planning of the city, we explore three scenarios: business-as-usual scenarios, farmland conservation scenarios, and wetland conservation scenarios. The results revealed the following: (1) Under the business-as-usual scenario, the rapid development of Fuyuan City showed the characteristics of the continued expansion of urban area and the reduction of farmland and wetland area in 2020 compared with 2010. (2) Under farmland conservation scenarios, farmland was well protected and stable, while construction land expansion was restricted. (3) Under wetland conservation scenarios, wetland increased dramatically, which mainly derived from farmland, grassland, and unused land. According to the result, optimized countermeasures are proposed to balance the coordinated development of farmland and wetlands, to deepen the multiperiod planning of land use in Fuyuan City and to provide data support and a basis for decision-making.