A numerical model (individual-based model) to describe ecosystem dynamics is proposed. The ecosystem is partitioned into the same time and space scale levels and the partitions at different levels are connected through transfer of mass. The partitioned system is expressed as aggregates of three-dimensional cells. Within the cells, nutrient intake, excretion, growth, reproduction, death, and movement of individual organisms are executed in accordance with the model rules. The mass transfer due to metabolic processes of organisms, including energy dissipation (efficiency) is described by difference equations. Movement to neighboring cells occurs through diffusion for substances, and through expansion of habitat range and migration in organisms. This individual-based model was applied to an experimental microecosystem (microcosm) derived from an aquatic ecosystem. This model was demonstrated to be applicable to descriptions from the micro behavior of individuals to macro system formation.