The molecular mechanism of the large electrocaloric effect in ferroelectric vinylidene difluoride-based polymers was proposed. The mechanism involves the electric field-induced phase transition between the ferroelectric β-phase and the paraelectric conformationally disordered (condis) phase. The condis phase is characterized by the absence of a three-dimensional crystallographic order: there is only two-dimensional translational symmetry in the plane perpendicular to the chain direction. Due to conformational disorder, the entropy of the condis phase is higher than that of the β-phase. A high entropy change at the transition from the β to the condis phase causes a large electrocaloric effect. Molecular dynamics simulations of the poly(vinylidene fluoride-co-trifluoroethylene) (poly(VDF-co-TrFE)) copolymer and poly(vinylidene fluoride–ter–trifluoroethylene–ter–chlorofluoroethylene) (poly(VDF-ter-TrFE-ter-CFE)) and poly(vinylidene fluoride-ter-trifluoroethylene-ter-chlorotrifluoroethylene) (poly(VDF-ter-TrFE-ter-CTFE)) terpolymers were performed. The electrocaloric effect was determined from simulations using two techniques: (i) direct calculation of the temperature drop in adiabatic conditions and (ii) calculation of the entropy difference between β and condis phases from the pair histograms of dihedral angles. Both techniques predict similar temperature drops that validate the proposed molecular mechanism.