We propose the approach to 3-D modeling of the electromagnetic (EM) field in time-domain airborne EM problems in complex media including rugged topography and curved borders between the geological layers, target objects of different shapes, lateral inhomogeneity within subhorizontal layers. For discretization of the electromagnetic field in space, the vector finite element method is used. We propose the approach to generating the optimized non-conforming finite element meshes with hexahedral cells in which several finite elements can be attached to the face of the other finite element which allows achieving the significant reduction of computational costs in comparison with the regular meshes on which the numerical solution has the same accuracy. The optimized non-conforming finite element mesh in a complex medium with the topography and curved borders of layers is generated with the use of special transformations. The method of constructing the finite element approximations on these non-conforming hexahedral meshes is proposed. For discretization of the electromagnetic field in time, the implicit three-point scheme “with backward overstepping” is proposed. For solving the finite element SLAE, we use the direct solver PARDISO the effectiveness of which is achieved due to the use of time stepping with a piecewise constant step and grouping the calculations of the electromagnetic field in time steps and transmitter positions. In order to increase the accuracy of calculating the signal in the receiver, a special procedure of smoothing the magnetic field B in space and special scheme of approximating the derivative of B in time are proposed. The verification of the proposed approaches is performed using the solution for the 1-D model and solutions for 3-D models obtained by other authors. We present the results of the comparative analysis of different time schemes in finite element calculating the electromagnetic field and in calculating the signal (in the form of EMF) in the receiver and choose the optimal step and the number of subintervals with the constant steps into which the entire modeling time interval is divided. We perform the comparative analysis of stair-like approximation of curved surfaces with the use of rectangular parallelepipeds and approximation with the use of the hexahedral elements and choose the optimal parameters of generating the finite element meshes. We present the results of the analysis of the possibility of replacing the model with topography with the “flat” 3-D model in which the topography is taken into account by correcting the airborne system height. For the “flat” 3-D model, we present the results of the analysis of the computational effectiveness through the use of the primary-secondary field approach with automatic choice of a horizontally-layered medium for calculating the primary field. For the complex geolelectrical model with topography, laterally-inhomogeneous overburden with curved boundaries, target objects under overburden and for a great number of airborne system positions, the computational costs are presented for sequential and parallel modes for modeling time from 0.01 ms to 1 ms and 10 ms. We present the analysis of the topography effect, the influence of the inhomogeneities in the overburden and target objects in the complex media and show that in this conditions, to discover the target objects using the form of the signal is practically impossible, i.e. in order to discover the target objects in these complex media, it is required to perform a very fine 3-D interpretation for carrying out of which fast and high accuracy forward 3-D modeling is of great importance. We obtain that for calculating the field for one transmitter and the entire modeling time interval in the sequential mode on one core of PC with processor Intel i7-8700K CPU of 3.7 GHz and 32 GB of DRAM, the required computational time is about 4–6 s. The required computational time in the parallel mode with the use of six cores of this PC is about 0.65–1 s.