Pathology reveals the complex changes of biological tissue development, differentiation, maturation, and apoptosis from a micro perspective. Single-cell analysis technology provides more information for the study of complex system of pathology. Tumor is a complex ecosystem composed of tumor cells and their surrounding microenvironment. In pathology, the cells in tumors are different, with different distribution and physiological functions, and are regulated by themselves, their surrounding environment and treatment methods, forming a complex system. Using the causal determination method in complex systems, we can reveal the complex regulatory role of a single cell, and the causal relationships between different types of tumor cells and patient treatment regimens, treatment effects, recurrence, and survival time. Taking tumor as an example, in this article we expound the significance and research methods of single-cell pathology based on causality in complex systems.