Lightning discharges, including cloud-to-ground (CG) and intracloud (IC) lightning, are known to emit electromagnetic pulses (EMPs) in a wide frequency band ranging from few Hz up to hundreds MHz [1]. During the breakdown and ionization processes (mostly from leader processes and streamers), there are strong emissions in the HF (3-30 MHz) and VHF (30-300 MHz) bands. When high currents occur in previously ionized channels (mostly from return strokes and the active stage of cloud flashes), the most powerful emissions concentrate in the very low frequency (3-30 kHz, VLF) and low frequency (30-300 kHz, LF) bands [2]. Among them, the VLF/LF waves of lightning discharges can propagate long distances with low attenuation by reflection between the ground surface and the lower D-region ionosphere (60-90 km), namely the so-called earth-ionosphere waveguide (EIWG). In order to investigate the lightning EMPs interaction with the ionosphere, a number of models and methods have been developed in the literature, such as the wave-hop (ray theory) method [3-6], the waveguide mode theory [7-9], or numerical methods such as the finite-difference-time-domain (FDTD) method [10-17] and the full-wave finite element method (FEM) [18,19]. Previous studies indicate that the amplitude and phase perturbation for lightning VLF/LF signals have a complicated relationship with the ionospheric D region parameters. The propagation of lightning EMPs between the earth ground surface and the lower D region ionosphere can be affected by many factors, such as the propagation distances [10,14,20], the ground conductivity [14,20], the electron and neutral particle densities [13,21,22], the Earth curvature [23,24], the presence of the Earth's magnetic field [22,25-27], and the presence of mountainous terrain [24]. In this chapter, we will first introduce the propagation theory of lightning EMPs interaction with the ionosphere on the basis of the full-wave FDTD method. We will then investigate the propagation effect of lightning radiated electromagnetic (EM) fields in the EIWG by considering the effect of the Earth curvature, the effect of the ground conductivity, and the effect of different ionospheric profiles. Finally, we will present applications, including (1) propagation of narrow bipolar events (NBEs) at different distances, (2) lightning electromagnetic fields propagation over mountainous terrain, and (3) the optical emissions of lightning-induced transient luminous events in the nonlinear D-region ionosphere.