Deep eutectic solvents (DESs) have been reported as a type of solvent for the controllable synthesis of metal nanostructures. Interestingly, flower-like palladium (Pd) nanoparticles composed of staggered nanosheets and nanospheres are spontaneously transformed into three-dimensional (3D) network nanostructures in choline chloride-urea DESs using ascorbic acid as a reducing agent. Systematic studies have been carried out to explore the formation mechanism, in which DESs itself acts as a solvent and soft template for the formation of 3D flower-like network nanostructures (FNNs). The amounts of hexadecyl trimethyl ammonium bromide and sodium hydroxide also play a crucial role in the anisotropic growth and generation of Pd-FNNs. The low electrocatalytic performance of Pd is one of the major challenges hindering the commercial application of fuel cells. Whereas, the 3D Pd-FNNs with lower surface energy and abundant grain boundaries exhibited the enhanced electrocatalytic activity and stability toward formic acid oxidation, by which the mass activity and specific activity were 2.7 and 1.4 times higher than those of commercial Pd black catalyst, respectively. Therefore, the current strategy provides a feasible route for the synthesis of unique Pd-based nanostructures.