As a new research field, biochip has enjoyed its rapid development in the past 10 years. Today, most of the biochip scanning systems are fluorescent confocal scanning systems. The conventional fluorescent confocal scanning system has few limits in some kind of biochips, such as cell-chip, tissue-chip and so on, because these biochips need a long working distance to add medicament or reagent in it real-time. The longer the working distance is, the more convenient to add the medicament or reagent. However, the conventional fluorescent confocal scanning system can’t have long working distance, especially when the system has high resolution and large aperture. In this paper, a dual-axis fluorescent confocal scanning system with a long working distance and high resolution has been presented. In the dual-axis fluorescent confocal scanning system, the incident light is tilt to the axis, which can decrease the bleaching of fluorescent induced by the laser. The working distance of the system is 15 mm and the numerical aperture is 0.35. The phase aberrations of objective lens, including the spherical aberrations and the chromatic aberrations corresponding to wavelength 532 nm, 570 nm, 635 nm, 670 nm, are corrected very well. The encircled energy diagram of the lens is good to the diffraction limit. The image spot diagram, the ray aberration fan diagram, the transverse ray fan plot and the modulation transfer function, are studied also. The image quality of the system designed in this paper is good enough to meet the practical requirements.