To achieve efficient and low-cost microalgae harvesting, investigations were conducted on the harvesting efficiency and potential mechanisms of Chlorella sp. HQ by filamentous fungi using two strategies, fungal spore-assisted harvesting (FSH) and fungal pellet-assisted harvesting (FPH). Five of the 19 fungal species isolated from domestic sewage could form pellets, and Aspergillus niger HW8-1 comprised the highest harvesting efficiencies of 99.17 % and 88.70 % for FPH and FSH, respectively. FSH had 2–3 times more lipids and polysaccharides in fungus-alga pellets and caused richer saturated and monounsaturated fatty acids compared with FPH. Moreover, by optimizing the microalgae preculture time, glucose concentration, and microalgae initial density, the contents of high-value substances, such as lipids, polysaccharides, and proteins of fungus-alga pellets after FPH were improved from 5.96 %, 5.67 %, and 7.27 % to 20.18 %, 24.34 % and 10.48 %, respectively. Furthermore, fungal pellets secreted more extracellular polymeric substances (EPS) during FPH than those by FSH, which could chemisorb algal cells by lowering the surface potential of fungal pellets. FPH caused algal cells to cover the outside, which increased the light exposure area of algae, thereby increasing the photosynthesis rate, whereas FSH mainly captured microalgae physically through mycelium entanglement.