Quercetin shows a strong promotion on the setting of oil well cement paste, and is expected to be used to promote the setting of cement plug to block lost circulation formations. This paper studied the working mechanism of quercetin on the setting of oil well cement. In addition, the effect of quercetin on the hydration of oil well cement was evaluated. The setting times, thickening times, rheological properties and compressive strengths of cement pastes containing quercetin were evaluated. Isothermal calorimetry (ICC), adsorption capacity, filtrate analysis, X-ray diffraction (XRD), thermogravimetric analysis (TGA), mercury intrusion porosimetry (MIP) and scanning electron microscope (SEM) were conducted to investigate the working mechanism. Results showed that quercetin promoted the dissolution of the gypsum. When the dosage reached 0.100% by weight of cement, Calcium ions quickly reached supersaturation and a lot of lamellar-structure portlandite generated, promoting the setting of cement paste. With 0.100% quercetin addition, the cement paste finally set in 50 min at 20 °C. In addition, quercetin had a large adsorption capacity for cement particles. As a result, the cement hydration was delayed and the compressive strength of hardened cement was reduced. Although quercetin is not conducive to cement hydration, its outstanding set accelerating effect and the ability to improve fluidity are beneficial to block lost circulation formations.