In Taiwan, the phenomenon of illegal factories on agricultural land is prevailing. As a result, the government attempts to implement a series of handling approaches, trying to solve this problem. However, the current government’s handling approaches are merely focusing on the consideration of economic aspect, and putting less attention on ecological and environmental aspects. If the ecological aspect can be taken into consideration in illegal factories handling approaches, it will help planners when formulating spatial planning policies. As a result, this paper attempts to simulate several handling approaches scenarios based on current handling approaches of illegal factories. We apply InVEST to estimate the amount of ecosystem services of each scenarios. Then, we use spatial autocorrelation (LISA) to identify the spatial change of different ecosystem services. After empirical research, it is found that in the case of handling approaches of illegal factories, it is recommended to implement the growth management plan scenario to accommodate illegal factories near the existing development area, which reduces the impact of scattered factories’ negative effect on multiple ecosystem services. This article uses scenario simulation and spatial autocorrelation to examine the effect of different illegal factories handling approaches, and it explores the impact of the handling approaches on the amount and location change of multiple ecosystem services. Finally, this article hopes to give suggestions for further illegal factories handling approaches in Taiwan.