Nanoparticles (NPs) can be incorporated into hydrogels to obtain multifunctional hybrid systems to meet the delivery needs of different drugs. However, the stability of NPs in hydrogels is rarely revealed. In this article, we tried to explore the underlying mechanism of an interesting phenomenon that poly(lactic-co-glycolic acid) (PLGA) nanoparticles (PNPs) could flocculate and deposit in Pluronic F127 (F127) hydrogels at 4 °C. The results showed that this flocculation was relevant to the type of emulsifier formulated in PNPs, the particle materials and the F127 concentration, but independent of PLGA polymer end groups. Exactly, PNPs containing polyvinyl alcohol (PVA) as the emulsifier flocculated in F127 solution with a concentration above 15 %. The flocculated PNPs possessed increased particle size, decreased zeta potential, reduced hydrophobicity and an obvious coating layer, and these characteristics could be restored almost to the original state after two washes of flocculated PNPs with water. Moreover, the flocculation had no impact on the long-term size stability and drug-loading capacity of PNPs, and F127-treated PNPs showed improved cellular uptake than untreated PNPs. These results provide the evidence that adsorption of high concentrations of F127 on the surface of PNPs/PVA may lead to flocculation, and the flocculation is reversible by simply washing the flocs with water. To the best of our knowledge, this is the first study to scientifically explore the stability of PNPs in F127 hydrogels, providing theoretical and experimental support for the rational design and further development of nanoparticle-hydrogel composite.