Lotus Receptaculum Nelumbinis has been sparking wide research interests due to its rich phenolic compounds. In the present work, ultrasonic-assisted extraction coupled with glycerol was employed to extract phenolic compounds from Receptaculum Nelumbinis and the process was optimized using a response surface methodology with Box-Behnken design (BBD). The optimal conditions for the total phenolic content (TPC) extract were obtained: glycerol concentration of 40%, an extraction temperature of 66 °C, ultrasonic time of 44 min, and the solvent-to-solid ratio of 55 mL/g. Under these optimum extraction conditions, the extraction yield of TPC was 92.84 ± 2.13 mg gallic acid equivalents (GAE) /g. Besides, the antioxidant activities demonstrated the ability of free radical scavenging by four different methods that included 2,2-Diphenyl-1-picrylhydrazyl (DPPH), ferric reducing antioxidant power (FRAP), 2,2′-azinobis(3-ethylbenzothiazoline-6-sulfonic acid) (ABTS), and reducing activity (RA) were 459.73 ± 7.07, 529.97 ± 7.30, 907.61 ± 20.28, and 983.66 ± 11.80 μmol TE/g, respectively. Six phenolic compounds were identified by ultra-high pressure liquid chromatography combined with triple-time-of-flight mass spectrophotometry (UPLC-Triple-TOF/MS) from the extracts. Meanwhile, Fourier transform infrared (FTIR) was conducted to identify the characteristic functional groups of the extracts and thus reflected the presence of polyphenols and flavonoids. Scanning electron microscopy (SEM) illustrated the microstructure difference of four treatments, which might explain the relationships between antioxidant activities and the structures of phenolic compounds.