The exchange bias phenomenon, inherent in exchange‐coupled ferromagnetic and antiferromagnetic systems, has intrigued researchers for decades. Van der Waals materials, with their layered structures, offer an ideal platform for exploring exchange bias. However, effectively manipulating exchange bias in van der Waals heterostructures remains challenging. This study investigates the origin of exchange bias in MnPS3/Fe3GeTe2 van der Waals heterostructures, demonstrating a method to modulate nearly 1000% variation in magnitude through simple thermal cycling. Despite the compensated interfacial spin configuration of MnPS3, a substantial 170 mT exchange bias is observed at 5 K, one of the largest observed in van der Waals heterostructures. This significant exchange bias is linked to anomalous weak ferromagnetic ordering in MnPS3 below 40 K. The tunability of exchange bias during thermal cycling is attributed to the amorphization and changes in the van der Waals gap during field cooling. The findings highlight a robust and adjustable exchange bias in van der Waals heterostructures, presenting a straightforward method to enhance other interface‐related spintronic phenomena for practical applications. Detailed interface analysis reveals atom migration between layers, forming amorphous regions on either side of the van der Waals gap, emphasizing the importance of precise interface characterization in these heterostructures.