The interaction between electromagnetic microwave field and biomacromolecule is not commonly understood, and the existence of the ‘microwave effects’ has been controversial. Herein, the aggregation behavior of fish myofibrillar proteins (MPs) induced by microwave heating (MW) and water bath heating (WB) was studied by using a range of electron microscopy techniques, including scanning electron microscope, cryo-SEM, atomic force microscopy, transmission electron microscope, and cryo-electron microscope. Through these methods, we hope to explore this issue from a multi-scale and dimensional perspective. In this communication, the unusual aggregation behavior of salt-soluble MPs under microwave irradiation was reported for the first time by controlling the same time–temperature heating curve with WB, yielding a dispersive and irregular structure with smaller particle size, subsequently generated a more stable, denser, and well-structured network. However, regional agglomeration behavior is more remarkable in WB treatment, which can lead to structural instability. These findings explained why microwaves can obtain protein gel with superior gel strength than WB from the structural perspective.