Although the antifouling modification of polyvinylidene fluoride (PVDF) membrane has attracted much attentions recently, the underlying fouling/antifouling mechanism of the PVDF membranes having different polymorphs have rarely been mentioned. In this study, two PVDF membranes with similar pore structure but distinct polymorphs were prepared, and their antifouling performance was systematically investigated by using synthetic solutions containing complex foulants relevant to surface water sources (e.g., humic acid, bovine serum albumin and dextran). A remarkable correlation between PVDF polymorph, membrane surface chemistry and fouling resistance was observed, demonstrating the exceptional ability of β-PVDF phase (i.e., β-PVDF membrane) in fouling mitigations when compared to α-PVDF phase (i.e., α-PVDF membrane). In order to unravel the fouling mechanism of PVDF membrane having different polymorphs, interaction forces between foulant-coated particle probes, simulating foulant molecules, and each membrane surface were measured by AFM and theoretical calculated depended on surface energy components. It is clearly shown that the enhanced fouling resistance of β-PVDF membrane was mainly driven by the reduced adhesion tendency of foulants, which could further attribute to the strong electron donor monopolarity of β-PVDF phase (γAB− = 25.3 mJ/m2) compared to α-PVDF phase (γAB− = 3.3 mJ/m2). Moreover, for each SSW-fouled membrane, depth profiling of the external fouling layer and composition of the extracted internal foulants were carefully investigated by variable angle FTIR and UV–vis spectrometer, respectively, suggesting the strong relationship between membrane fouling behavior and membrane-foulant and foulant-foulant interactions. This work emphasized the selection of proper polymorph of PVDF membrane should be valued so as to mitigate membrane fouling, and we anticipate the advantage of β-PVDF phase in membrane fouling control can boost the development of additive-free and sustainable antifouling strategy in future.