Fluorescence microscopy imaging of live cells has provided consistent monitoring of dynamic cellular activities and interactions. However, due to the limited adaptability of current live-cell imaging systems, portable cell imaging system has been adapted by broad strategies, including miniaturized fluorescence microscopy. Here, we provide a protocol for the construction and operational process of miniaturized modular-array fluorescence microscopy (MAM). The MAM system is built in a portable size (15 cm × 15 cm × 3 cm) and provides in situ cell imaging inside an incubator with a subcellular lateral resolution (~3 μm). We demonstrated the improved stability of the MAM system with fluorescent targets and live HeLa cells, enabling long-term imaging for 12 hours without the need for external support or post-processing. We believe the protocol could guide scientists to construct a compact portable fluorescence imaging system and perform time-lapse in situ single-cell imaging and analysis.