The structure–performance mechanism is essential to achieve comprehensive characteristics for advanced communication system. In the present work, F− ions were adopted to fabricated Li3Mg2NbO6-x/2Fx ceramics at a nitrogen atmosphere to modify dielectric characteristics. Correlation between bond characteristics, crystal structure and enhanced microwave dielectric characteristics was investigated through vibration analysis, P–V-L theory, Rietveld refinement, and First-principle calculations. Raman analysis and Rietveld refinement show that F− substitution led to a single phase. First-principle calculations indicates a high energy gap of 3.676 eV and p orbit contributed to Fermi energy. F− substitution led to the increase of Nb O bond ionicity and lattice energy, accounting for the variation in Q×f value and dielectric constant. The τf value was related to the expansion coefficient of the Li–O bond. Remarkably, the samples (x = 0.08) exhibited comprehensive dielectric characteristics with εr = 15.9, Q×f = 143,000 GHz and near-zero τf = −2.1 ppm/°C, proving an effective strategy for collaborative regulation. Based on structure simulation, 5G filter with ultra-low loss and high-suppression was designed through introducing transmission zeros from cross coupling. More specifically, a dielectric filter exhibited an interpolation loss of 0.2 dB at 3.3–3.6 GHz and high attenuations of 15 dB for 20 MHz outside the passband, verifying the feasibility for 5G applications.