Chlamydomonas reinhardtii possesses two flagella of equal length, making it an excellent model organism for investigating the flagellar size, flagellar genes, and flagellar assembly. However, due to its highly active in liquid medium through flagellar swing, monitoring flagellar assembly/disassembly kinetics in single living cells has been challenging over extended periods. This issue can be effectively addressed by utilizing microfluidic chips with their micron-scale structure and fluid control capabilities, offering precise screening or analysis with high throughput and sensitivity. Consequently, we present a microfluidics chip capable of immobilizing Chlamydomonas reinhardtii losslessly in situ to enable long-term observation of changes in the length of individual wild-type Chlamydomonas reinhardti’s flagella. By modifying the chip’s dimensions, it can also be employed to monitor alterations in the flagellar length of Chlamydomonas mutants of different sizes for a long time. Furthermore, we have integrated laser cutting technology into the microfluidic chip system to investigate how flagellar genes influence the regulation of Chlamydomonas’ flagellar assembly/disassembly.