In this study, a new design of a controllable micro-lens structure capable of the enhancement of LIF detection system has been demonstrated, which can be further integrated with buried optical fibers on a micro-CE chip for sample separation and detection. Two pneumatic side-chambers were placed between a micro-CE channel and an optical fiber channel. The intervals between the side-chamber and the microchannel were used to form two surfaces of the controllable micro-lens structure. Deformations of the two surfaces can be generated after pressurized index-matching fluid was injected into the pneumatic side-chambers. The side-chambers can be deflected as a double convex lens to focus both the excitation light source and the fluorescent emission signal. The profile and the focal length of the micro-lens structure can be actively adjusted by applying different liquid pressures so that biosamples with a low concentration can be detected. Using low-cost polymeric materials such as polydimethylsiloxane, rapid and reliable fabrication techniques involving standard lithography and replication process was employed for the formation of the proposed chip device. Experimental results revealed the controllable micro-lens structure can be successfully deformed as a convex lens to focus the laser light source and the collected fluorescence signal can be enhanced accordingly. The power amplitude of excitation laser light can be enhanced by 5.4-fold. FITC dye and DNA markers were then utilized for micro-CE testing. The results indicated that the signal amplitude could be enhanced 2.5-fold when compared to the case without the activation of the micro-lens. According to the experimental results, the developed device has a great potential to be integrated with other microfluidic devices for further biomedical applications.