There are a huge number, and abundant types, of microalgae in the ocean; and most of them have various values in many fields, such as food, medicine, energy, feed, etc. Therefore, how to identify and separation of microalgae cells quickly and effectively is a prerequisite for the microalgae research and utilization. Herein, we propose a microfluidic system that comprised microalgae cell separation, treatment and viability characterization. Specifically, the microfluidic separation function is based on the principle of deterministic lateral displacement (DLD), which can separate various microalgae species rapidly by their different sizes. Moreover, a concentration gradient generator is designed in this system to automatically produce gradient concentrations of chemical reagents to optimize the chemical treatment of samples. Finally, a single photon counter was used to evaluate the viability of treated microalgae based on laser-induced fluorescence from the intracellular chlorophyll of microalgae. To the best of our knowledge, this is the first laboratory prototype system combining DLD separation, concentration gradient generator and chlorophyll fluorescence detection technology for fast analysis and treatment of microalgae using marine samples. This study may inspire other novel applications of micro-analytical devices for utilization of microalgae resources, marine ecological environment protection and ship ballast water management.