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This paper describes the implementation and optimization of a dual-confocal autofocusing system that can easily describe a real-time position by measuring the response signal (i.e., intensity) of the front and the rear focal points of the system. This is a new and systematic design strategy that would make it possible to use this system for other applications while retrieving their characteristic curves experimentally; there is even a good chance of this technique becoming the gold standard for optimizing these dual-confocal configurations. We adopt two indexes to predict our system performance and discover that the rear focal position and its physical design are major factors. A laboratory-built prototype was constructed and demonstrated to ensure that its optimization was valid. The experimental results showed that a total optical difference from 150 to 400 mm significantly affected the effective volume of our designed autofocusing system. The results also showed that the sensitivity of the dual-confocal autofocusing system is affected more by the position of the rear focal point than the position of the front focal point. The final optimizing setup indicated that the rear focal length and the front focal length should be set at 200 and 100 mm, respectively. In addition, the characteristic curve between the focus error signal and its position could successfully define the exact position by a polynomial equation of the sixth order, meaning that the system can be straightforwardly applied to an accurate micro-optical auto-focusing system.