In recent years, ecological systems such as forests, farmlands, and wetlands have witnessed an alarming rate of encroachment owing to indiscriminate urban development. This has resulted in the emergence of serious environmental and ecological issues such as air pollution, heat island formation, and groundwater contamination. Therefore, rational urban growth is becoming an increasingly important focus area for decision makers. Urban land planning is one of the most important means for inducing rational urban growth. However, most urban planning scenarios are based on only historical sprawl trends or traditional supply-demand balance; hence, they tend to ignore potential ecological and environmental issues. Consequently, optimal urban growth patterns that consider ecological conservation are attracting considerable interest from researchers and administrative decision makers. The conservation of ecologically sensitive areas plays a key role in environmental protection. Thus, harmonizing urban sprawling with the conservation of ecologically sensitive areas can be viewed as a binary compatibility planning problem. Here, we employ a geographical simulation and optimization system (GeoSOS) to apply complex spatial techniques to the analysis of the conflict between urban development and ecological protection. Current urban planning strategies and historical development rules are both considered to generate ecologically harmonious urban growth patterns, with the objective of providing a feasible decision-making framework for urban planning. The main procedures can be described as follows: First, ecologically sensitive areas such as rivers and mountains are marked out on the basis of actual development demands. Next, the spatial conservation priority for ecologically sensitive areas is calculated using the minimum cumulative resistance (MCR) model. Second, urban sprawl patterns are simulated on the basis of historical rules using the cellular automata (CA) model. The conflict between urban development and the conservation of ecologically sensitive areas is then identified according to the simulation results; potential ecological issues are also considered for urban planning. Third, a trade-off between urban development and ecological protection is considered when re-evaluating ecological suitability for urban sprawling; then, an ecologically harmonious pattern is accordingly generated using the ant colony optimization (ACO) model. Guangzhou City, located in the Pearl River Delta, China, is selected for a case study to validate the feasibility of the proposed analysis framework. Remote sensing images collected in the years 2000, 2005, and 2010 are used to obtain urban land information and to identify ecologically sensitive areas. Topographical and socio-economic data as well as transportation networks are used to analyze the locational conditions for urban development. In addition, a schematic map of land use in 2005 and current urban planning documents are used as important reference materials. The harmonious planning procedure supported by GeoSOS is described and verified in detail. An optimal urban growth pattern that considers ecological protection is generated using the ACO model, and it is compared with the simulation pattern obtained using the CA model. Results indicate that the former is a closer approximation of actual urban development than the latter and results in less environmental degradation. Spatial optimization techniques can be also used as efficient auxiliary tools for decision-making. The binary compatibility framework based on GeoSOS can serve as an additional technical reference for urban planning.