Microalgae harvest and lipid accumulation were important factors influencing commercialized development of microalgae biodiesel. Spontaneous flocculation was an ideal method in microalgae harvest, but few rich lipid microalgae could be harvested by spontaneous flocculation. Rich lipid alga Heveochlorella sp. Yu has a characteristic of spontaneous flocculation to be harvested. Heveochlorella sp. Yu has high lipid productivity (105.24 mg L−1 d−1) and fine spontaneous flocculation efficiency (82.93 %, 2 h) on early stationary phase (day 9). The polysaccharides consisting of glucose, mannose, galactose, rhamnose and fructose (8.67:4.90:3.27:2.16:1) in loose-bound extracellular polymeric substance (LB-EPS) might make great contribution in microalgae flocculation. Meanwhile, the zeta potential close to zero was also beneficial to microalgae flocculation. Besides, the adhesion free energy related with cells adhesion was detected by thermomechanical analysis. Afterward, Extended Derjaguin-Landau-Verwey-Overbeek (XDLVO) theory was utilized to quantitatively evaluate short-range interactions involved in the spontaneous aggregation among cells. Collectively, biophysical analyses indicated that content and composition of EPS, Zeta potential, thermodynamic parameter and total interaction based on XDLVO theory were closely connected with spontaneous flocculation in microalga Yu. Our study provided a harvest-simplified process of rich microalgae, which proposes a new idea for commercial development of microalgae biodiesel.