SummaryA cell‐free (CF) technology and unmanned aerial vehicles (UAVs) acting as aerial relay stations (ARSs) are gradually viewed as viable technologies for usage in sixth‐generation (6G) wireless networks owing to their outstanding advantages, such as large coverage, uniform service quality, huge connections, flexible deployment in all geographical areas, and high line‐of‐sight (LoS) probability. As a result, the combination of the CF model and UAVs is suitable for densely populated urban areas, shopping malls, festivals, and locations with complex geography. Furthermore, the integration of the CF model and UAV communication can improve system quality and is considered an entirely new research direction as there is no comprehensive investigation of this combined model. In this study, we investigate the quality of the multi‐ARS CF communication system, where ARSs are equipped with multiple antennas and stochastic distribution within a specific region to simultaneously serve numerous ground users. We establish a closed‐form formulation for the uplink and downlink throughput of individual users by using the matched filtering method and conjugate beamforming technology, respectively. Moreover, we propose a novel method to optimize the pilot and data transmission power coefficients for improving channel estimation and increasing throughput per user, thereby ensuring a high quality of service. The power optimization method is executed via the successive convex approximation (SCA) method, second‐order cone program (SOCP), and linear program. We evaluate system performance according to the cumulative distribution function (CDF) of user throughput based on various parameters, such as the number of users, the number of ARSs, and the length of pilot sequences. The analytical findings also reveal that the system with the proposed power optimization method is always superior to the system without the proposed method in both uplink and downlink.