Emitter clogging is a bottleneck to restrain the application and popularization of reclaimed water drip irrigation technology, and it is tightly related to the formation of biofilms attached on drip irrigation emitters. However, there is still no quantitative description about the relationship between biofilms components and emitter clogging. Based on the reclaimed water drip irrigation experiment, the characteristics of biofilms attached on 7 kinds of emitters under reclaimed water drip irrigation have been systematically explored with phospholipid fatty acids (PLFAs) and other microbiological testing methods, and quantitative relationship between biofilms components and emitter clogging was analyzed. The results showed that emitter clogging degree and biofilms components revealed an increasing trend with the drip irrigation system running, which could be regarded as the “quick-slow-quick-slow” increasing trend. Biofilms exhibited a rapid growth after restarting in the 2nd year. The dry weights (DWs), PLFAs, and extracellular polymers (EPS) of biofilms attached on the emitters could reach up to 0.133 g, 100.83 μg, and 1,645.04 μg, respectively, after accumulatively ran for 540 h. DWs of biofilms in different positions such as head, middle, and end parts of the lateral also revealed a increasing trend. Meanwhile, biofilms in the pressure-compensating emitters grew less than that in the non-pressure-compensating emitters. During the initial 540 h of the system running, DWs, PLFAs, and EPS of attached biofilms had a obvious negative linear correlation (R2 > 0.85) with emitter discharge ratio variation (Dra) and coefficient of uniformity (CU), which could describe the drip irrigation emitter clogging mechanism well. Furthermore, PLFAs reflected the type and quantity of microorganisms in attached biofilms, and sticky EPS secreted by microorganisms could link the microorganisms with absorbed particulates together and formed the stable biofilm structure. As PLFAs reflected the comprehensive effect of microorganisms, particulates and EPS on emitter clogging, and presented the highest negative linear correlation with Dra (R2 = 0.93), it is most appropriate to reflect emitter clogging mechanism. These results can provide a theoretical basis for exploring emitter clogging mechanism and promoting the application of reclaimed water drip irrigation technology.