The effect of fermentation strains (Lactiplantibacillus plantarum CQ01107 and Staphylococcus simulans CD207) on the binding properties of porcine myofibrillar proteins (MPs) to esters was investigated from two perspectives: metabolism degree and structural alterations. Results demonstrated that S. simulans could reduce the particle size and α-helix content of MPs, while simultaneously increasing the absolute zeta potential and active sulfhydryl content. This process decreased protein aggregation and facilitated the unfolding of MPs, thereby enhancing their binding to esters. Conversely, L. plantarum showed limited promotion, which might be related to its robust acid production and protein hydrolysis capacities. In addition, ethyl octanoate, with a longer carbon chain length, was found to have the highest binding capacity to MPs (28.38 %–41.59 %). Molecular docking results further revealed that the binding of the four esters to MPs was spontaneous, with ethyl octanoate exhibiting the lowest binding energy to MPs (−5.635 kcal/mol). The primary forces involved in the binding of the four selected esters to MPs were hydrophobic interactions, hydrogen bonding, and van der Waals forces. These findings can provide new insights into the mechanisms by which fermentation strains influence flavor formation in fermented foods.