Learning the micro-mechanisms of fluorinated polymers during mechanical response is more difficult than that of common polymers due to the unique intrinsic characteristics of the fluorine element. In this paper, we applied molecular dynamics simulations to study deformation mechanisms of poly(vinylidine fluoride-co-chlorotrifluoroethylene) during uniaxial tension. We analyzed the variations of individual energy components and structural distribution curves versus strain in addition to the commonly used stress-strain curves and microstructure evolutions during stretching. The elastic limit is ɛ = 0.02, ɛ = 0.06 is the yield point, ɛ = 0.24 is the termination of the softening, necking occurs at 0.24 < ɛ < 0.5, strain hardening occurs at 0.5 < ɛ < 2.6, and ɛ = 2.6 is the damage or brake point. The elastic behavior of the material does not rely on strain rate, the obvious effect of strain rate can be seen at the yield region and strain softening region, and the stress values are not influenced by strain rates at the softening and hardening stages. Overall, total potential energy is mainly correlated with non-bonded energy, and the proportion of ΔEcoul overwhelms all the others. The energy components are ordered: ΔEcoul > ΔEvdwl > > ΔEangle > ΔEdihed > ΔEbond. The chain conformation at yield point is almost unchanged compared with the pre-stretching conformation. The chain conformations at the end of strain softening changes more obviously than that at yield point. The molecular chains maintain random coil structure before strain hardening, and switch into a stretch chain conformation gradually during strain hardening. The maximum change in bond angle during the stretching process is F-C-H, the largest change in bond length is the C-Cl bond, and the largest change in dihedral angle is H-C-C-H. The change of non-bonded interaction in the poly(VDF-co-CTFE) system is much larger than the bonding interaction, and the main factor affecting bonding interaction is the change of angles. Graphical abstract Poly(vinylidine fluoride-co-chlorotrifluoroethylene) during tensionᅟ.