Coupling the effects of flexoelectricity with piezoelectricity has been proved to effectively harvest mechanical energy. In this study, a composition-graded core–shell structure (HAP@FAP) was prepared by surface-gradient F-doping in hydroxyapatite, which could introduce flexoelectricity by a built-in strain gradient. A flexoelectric-boosted piezoelectric response was demonstrated by piezoresponse force microscopy (PFM) characterization, showing that the piezoelectric constant of HAP@FAP was increased by 2.25 times via a lattice strain gradient induced by chemical heterogeneities derived from the unique composition-graded core–shell structure. Thus, the piezocatalytic activity of HAP@FAP for phenanthrene (PHE) degradation in soil was enhanced. This work provides a new strategy for the modification of piezoelectric catalysts for the remediation of organics-contaminated soils on industrial land.