In the rapidly evolving domain of Unmanned Aerial Vehicles (UAVs), precise altitude estimation remains a significant challenge, particularly for lightweight UAVs. This research presents an innovative approach to enhance altitude estimation accuracy for UAVs weighing under 2 kg without cameras, utilizing advanced AI Deep Learning algorithms. The primary novelty of this study lies in its unique integration of unsupervised and supervised learning techniques. By synergistically combining K-Means Clustering with a multiple-input deep learning regression-based model (DL-KMA), we have achieved substantial improvements in altitude estimation accuracy. This methodology represents a significant advancement over conventional approaches in UAV technology. Our experimental design involved comprehensive field data collection across two distinct altitude environments, employing a high-precision Digital Laser Distance Meter as the reference standard (Class II). This rigorous approach facilitated a thorough evaluation of our model’s performance across varied terrains, ensuring robust and reliable results. The outcomes of our study are particularly noteworthy, with the model demonstrating remarkably low Mean Squared Error (MSE) values across all data clusters, ranging from 0.011 to 0.072. These results not only indicate significant improvements over traditional methods, but also establish a new benchmark in UAVs altitude estimation accuracy. A key innovation in our approach is the elimination of costly additional hardware such as Light Detection and Ranging (LiDAR), offering a cost-effective, software-based solution. This advancement has broad implications, enhancing the accessibility of advanced UAVs technology and expanding its potential applications across diverse sectors including precision agriculture, urban planning, and emergency response. This research represents a significant contribution to the integration of AI and UAVs technology, potentially unlocking new possibilities in UAVs applications. By enhancing the capabilities of lightweight UAVs, we are not merely improving a technical aspect, but revolutionizing the potential applications of UAVs across industries. Our work sets the stage for safer, more reliable, and precise UAVs operations, marking a pivotal moment in the evolution of aerial technology in an increasingly UAV-dependent world.