This paper proposes a new approach on aiding for optimizing the design, operations, and maintenance planning of new and existing large-scale composting facilities. Numerical modeling on mass/energy transport, degradation process, and turning/shifting processes was discussed. The models are integrated with the 3D finite element method based system, which is able to solve for mass/energy distribution fields influenced by biological activities at each corresponding location and interaction with arbitrary environment. As a result, designing and planning for more cost-effective and better performance facilities without performing trail tests shall become possible.