Computer simulation of continuous chaotic systems is usually performed using numerical methods. The discretization may introduce new properties into finite-difference models compared to their continuous prototypes and can therefore lead to new types of dynamical behavior exhibited by discrete chaotic systems. It is known that one can control the dynamics of a discrete system using a special class of integration methods. One of the applications of such a phenomenon is chaos-based communication systems, which have recently attracted attention due to their high covertness and broadband transmission capability. Proper modulation of chaotic carrier signals is one of the key problems in chaos-based communication system design. It is challenging to modulate and demodulate a chaotic signal in the same way as a conventional signal due to its noise-like shape and broadband characteristics. Therefore, the development of new modulation–demodulation techniques is of great interest in the field. One possible approach here is to use adaptive numerical integration, which allows control of the properties of the finite-difference chaotic model. In this study, we describe a novel modulation technique for chaos-based communication systems based on generalized explicit second-order Runge–Kutta methods. We use a specially designed test bench to evaluate the efficiency of the proposed modulation method and compare it with state-of-the-art solutions. Experimental results show that the proposed modulation technique outperforms the conventional parametric modulation method in both coverage and noise immunity. The obtained results can be efficiently applied to the design of advanced chaos-based communication systems as well as being used to improve existing architectures.