Forest Simulation and Optimization System (FSOS) model has been widely used in British Columbia of Canada and in Changbai Mountains of China. This model is based on the viewpoint of harmonized and balanced management of forest resources and the application of simulated annealing optimized algorithms in arranging forest management schemes, aimed to realize the sustainable and harmonized development of forest resources multiple objective management and to transform forests to their desired status. The multiple functions (or the multiple objectives) in the FSOS model include water storage and purification, carbon sequestration, wildlife habitat protection, biodiversity conservation, visual landscape quality, and timber production, and the desired forest status is comprehensively defined by experts, environmental organizations, and government policies. This paper introduced in detail the simulated annealing algorithms in FSOS, including solution representation, evaluations, and transitions, and the potential applications of the algorithms in forest ecosystem planning, aimed to provide helps to the planning and management of forest resources and to the governments to quantify, analyze, and manage the forest resources, effectively monitor forest operations, and achieve the sustainable development of forest ecosystem.