The difficulty to generate and control large strain gradients in materials hinders the investigation and application of flexoelectricity and flexomagnetism. This work demonstrates that thermal expansion can be used to induce very large non‐uniform strains at the nanoscale, resulting in giant strain gradients at moderate temperatures. This is demonstrated in a nanopatterned multiferroic hybrid layer consisting of a regular array of ferromagnetic metallic nanocylinders embedded in a ferroelectric polymer matrix. The thermally‐induced strain gradients can fully depolarize the ferroelectric component, and modify the magnetization of the ferromagnetic component via flexoelectric and flexomagnetic effects, respectively. Finite‐element analysis provides a quantitative view on thermal expansion‐induced strains and strain gradients supporting the experimental findings. This work shows that nanoscale thermal strain engineering provides an additional degree of freedom to control electrical polarization and magnetization, which paves the way for the design and operation of novel functional devices and nanostructures.