Microscopic imaging is a critical tool in scientific research, biomedical studies, and engineering applications, with an urgent need for system miniaturization and rapid, precision autofocus techniques. However, traditional microscopes and autofocus methods face hardware limitations and slow software speeds in achieving this goal. In response, this paper proposes the implementation of an adaptive Liquid Lens Microscope System utilizing Deep Reinforcement Learning-based Autofocus (DRLAF). The proposed study employs a custom-made liquid lens with a rapid zoom response, which is treated as an “agent.” Raw images are utilized as the “state”, with voltage adjustments representing the “actions.” Deep reinforcement learning is employed to learn the focusing strategy directly from captured images, achieving end-to-end autofocus. In contrast to methodologies that rely exclusively on sharpness assessment as a model’s labels or inputs, our approach involved the development of a targeted reward function, which has proven to markedly enhance the performance in microscope autofocus tasks. We explored various action group design methods and improved the microscope autofocus speed to an average of 3.15 time steps. Additionally, parallel “state” dataset lists with random sampling training are proposed which enhances the model’s adaptability to unknown samples, thereby improving its generalization capability. The experimental results demonstrate that the proposed liquid lens microscope with DRLAF exhibits high robustness, achieving a 79% increase in speed compared to traditional search algorithms, a 97.2% success rate, and enhanced generalization compared to other deep learning methods.