Microfluidic flow cytometry (MFCM) is considered to be an effective substitute for traditional flow cytometry, because of its advantages in terms of higher integration, smaller device size, lower cost, and higher cell sorting activity. However, MFCM still faces challenges in balancing parameters such as sorting throughput, viability, sorting efficiency, and cost. Here, we demonstrate a cost-effective and high-performance microfluidic cytometry cell sorting system, along with a customized microfluidic chip that integrates hydrodynamic focusing, droplet encapsulation, and sorting for precise cell manipulation. An innovative photon incremental counting-based fluorescence detection method is proposed, which requires only one-fiftieth of the data compared to traditional methods. This significantly simplifies the structure of the system and substantially reduces costs. The system exhibits detection recoveries exceeding 95% across sample solution flow rates ranging from 10 to 80 μL min