In this study, "Integrated in situ analyzer-ATP (IISA-ATP)" which is to estimate microbial activities in deep-sea environments has been developed. On the system, a microfluidic device is used as a core element to perform a bioluminescent (luciferin-luciferase) reaction for ATP quantification. The microfluidic device has a coil-shaped microchannel for photo intensity measurement. In this paper, concept of the IISA-ATP and optimization process of the microchannel design are presented. As a result of the microchannel design and flow rate optimization, 2 pM to 2 x 104 pM (20 nM) of ATP was successfully quantified.