This paper deals with complex system theory to describe guerrilla warfare situation using EINSTein (Enhanced ISAAC Neural Simulation Tool) simulation model. EINSTein model is an agent-based artificial "laboratory" for exploring self-organized emergent behavior in land combat. Many studies have shown that existing Lanchester equations used in most guerrilla warfare models do not describe changes of combat units, real guerrilla warfare situation and qualitative factors in combat. Future warfare will be information warfare with various weapon system and complex combat units. We have compared and tested results with Lanchester models and EINSTein model. And the EINSTein model has been applied and analyzed to guerrilla warfare model (C4I facilities, coastal, urbanized terrain critical facilities defense). The results show that the EINSTein model has a possibility to apply and analyze guerrilla warfare more properly than Lanchester models.