The effects of thermosonication (TS) washing at varying multi-frequencies in comparison to ultrasonication (US) and water washing (as a control) on the fresh-cut lotus root phenolics accumulation and the storage quality characteristics were explored. The relationships between free phenols (FPs), bound phenols (BPs), total phenolic content (TPC), and total antioxidant capacity were also revealed. Thermosonication increased the free phenols and total phenolic content, with the thermosonication of 20 + 40 + 60 kHz showing the most significant effect, and TS predominantly improved the total antioxidant capacity. Thermosonication promoted phenylalanine ammonia-lyase (PAL) activity and inhibited polyphenol peroxidase (POD) activity. The color analysis showed the thermosonicated samples exhibited the lowest value of ΔE and the browning degree. Thermosonication substantially increased weight loss and firmness, while reducing the levels of malondialdehyde (MDA) and Vitamin C (VC) compared to control. Overall, TS washing can increase the phenolic content of fresh-cut lotus root while preserving its antioxidant capacity and qualitative characteristics.