An effective and original strategy described as two-dimensional encapsulation is designed to prepare a high-performance fluorinated carbon cathode composed of a fluorinated carbon/graphdiyne heterostructure (CFx/GDY). The GDY layers of CFx/GDY strengthened the three-dimensional contacts between the CFx particles and additive, achieving outstanding charge transport kinetics and accelerating the lithium-ion diffusion dynamic behavior. The obtained electrodes exhibited a significantly enhanced voltage platform of ∼2.5 V, improved battery rate performance (5C, 621.6 mA h g-1) and energy density with 2039.3 W h kg-1. The excellent storage kinetics can be ascribed to the electronic structure modulation of fluorinated carbon from GDY, and the hierarchical porosity of GDY to create an effective, stable electron transfer and robust ion transportation. Our results demonstrated that two-dimensional GDY encapsulation has enormous potential in improving the performance of lithium primary batteries.