Flexible magnetoelectric (ME) generators gained immense interest due to the broad applications in wearable and Internet of Things (IoT)-based devices. The key to achieving high energy conversion performance of 0-3 type ME composite films is the prevention of filler aggregation in the polymer matrix and accessing the full potential of intrinsic properties of filler. To achieve high performance, a flexible ME composite film was fabricated by homogeneous distribution of magnetostrictive CoFe2O4-BaTiO3 core-shell (CBCS) fillers into piezoelectric polyvinylidene fluoride (PVDF) polymer. The ME composite film generates an enhanced energy conversion efficiency by optimizing the shell thickness of CBCS and maximizing the electroactive β-phase at the BaTiO3 shell-PVDF interfacial region. The observed ME coefficient of the film reached up to 710 mV/cm∙Oe. Multiphysics simulations based on the finite element analysis were adopted to investigate the role of BaTiO3 shell thickness on the performance of ME film. This study paves the way to achieve higher filler loading content in the ME composite films to develop an efficient, flexible ME generator for eco-friendly permanent power sources.