Inferring reward functions from demonstrations is a key challenge in reinforcement learning (RL), particularly in multi-agent RL (MARL), where large joint state-action spaces and complex inter-agent interactions complicate the task. While prior single-agent studies have explored recovering reward functions and policies from human preferences, similar work in MARL is limited. Existing methods often involve separate stages of supervised reward learning and MARL algorithms, leading to unstable training. In this work, we introduce a novel end-to-end preference-based learning framework for cooperative MARL, leveraging the underlying connection between reward functions and soft Q-functions. Our approach uses a carefully-designed multi-agent value decomposition strategy to improve training efficiency. Extensive experiments on SMAC and MAMuJoCo benchmarks show that our algorithm outperforms existing methods across various tasks.