To fabricate pork myosin nano-aggregates and investigate the effect of aggregation modes on emulsified gels, the surface charge, aggregate size, characteristic morphology, protein conformation, chemical forces and microstructures were measured at different pHs and ionic strength during the heat treatment of 75 °C for 30 min. The results showed three kinds of aggregation modes were formed, including fibril aggregation, amorphous aggregation and hydrogel aggregation, in which the characteristic morphology of myosin aggregates was fibrous strand-like, spongy, hippocampus-like and network-like, respectively. The flexible filaments were formed with higher positive charges and larger sizes at pH 3.0, and in contrast at pH 9.0 the hydrogel was formed with higher negative charges and smaller sizes. As the morphology changed from fibrous strand-like to network-like, α-helix significantly increased but β-sheet, β-turn and random coil significantly decreased (P < 0.05), implying that the characteristic morphology was affected by the changes in secondary structures. The surface hydrophobicity significantly increased along with pH shift from 5.0 to 9.0, and at pH 3.0 surface hydrophobicity was the highest, however, reactive sulphydryl and total sulphydryl contents both significantly decreased and were the lowest at pH 3.0. The results indicated that the exposure of hydrophobic groups and transformation of sulphydryl into disulfide bonds occurred, and the differences in characteristic morphology and aggregation mode may be ascribed to hydrophobic binding sites. In addition, the emulsions formed characteristic gel structures that corresponded to characteristic morphology of aggregates, in which hydrophobic binding sites, secondary structures and chemical bonds changed emulsified gel structures that were related to viscoelastic properties and emulsion stability.