It is difficult to effectively eradicate C. albicans using traditional antifungal agents, mainly because the low permeability of the C. albicans cell wall creates strong drug resistance. The aim of this study was to investigate the synergistic fungicidal effect and the underlying mechanisms of low-frequency and low-intensity ultrasound combined with a treatment of amphotericin B-loaded nanoparticles (AmB-NPs) against C. albicans. AmB-NPs were prepared by a poly(lactic-co-glycolic acid) (PLGA) double emulsion method. C. albicans was treated by AmB-NPs combined with 42 kHz ultrasound irradiation at an intensity of 0.30 W/cm2 for 15 min. The results demonstrate that the application of ultrasound enhanced the antibacterial effectiveness of AmB-NPs (P < 0.01), and the antifungal efficiency increased significantly with increasing AmB concentration of drug-loaded nanoparticles under ultrasonic irradiation. Additionally, the mycelial morphology of C. albicans suffered from the most severe damage and loss of normal microbial morphology after the combined treatment of AmB-NPs and ultrasound, as revealed by electron microscope. Furthermore, we verified the safe use of low-frequency ultrasound on exposed skin and discussed the potential mechanism of ultrasound enhanced fungicidal activity. The results reveal that the mechanism may be associated with the ultrasound cavitation effect and an increase in intracellular reactive oxygen species.