While Large Language Model-based Multi-Agent Systems (MAS) consistently outperform single-agent systems on complex tasks, their intricate interactions introduce critical reliability challenges arising from communication dynamics and role dependencies. Existing Uncertainty Quantification methods, typically designed for single-turn outputs, fail to address the unique complexities of the MAS. Specifically, these methods struggle with three distinct challenges: the cascading uncertainty in multi-step reasoning, the variability of inter-agent communication paths, and the diversity of communication topologies. To bridge this gap, we introduce MATU, a novel framework that quantifies uncertainty through tensor decomposition. MATU moves beyond analyzing final text outputs by representing entire reasoning trajectories as embedding matrices and organizing multiple execution runs into a higher-order tensor. By applying tensor decomposition, we disentangle and quantify distinct sources of uncertainty, offering a comprehensive reliability measure that is generalizable across different agent structures. We provide comprehensive experiments to show that MATU effectively estimates holistic and robust uncertainty across diverse tasks and communication topologies.