The large eddy simulation model coupled with the modified Schnerr–Sauer cavitation model has been used to numerically simulate the unsteady cavitation and noncavitation flow of the three-dimensional NACA66 (National Advisory Committee for Aeronautics) hydrofoil under different operating conditions. The results show that the magnitude of the cavitation number plays a decisive role in the hydrofoil cavitation quasiperiodic phenomenon. The cavitation number of 1.25 is used as a typical working condition for analysis. Using the Ffowcs Williams–Hawkings acoustic analogy approach accompanied by the vorticity transport equation splitting, the growth and shedding of cavitation also lead to the growth and shedding of the vortex structure. The cavitation–vortex interaction is mainly influenced by the vortex stretching term and vortex dilatation term and amplitude of them are larger than 500. The baroclinic torque term may be responsible for generating vorticity during the cloud cavitation collapse and has a lower amplitude about 200. The cavity volume acceleration is the main influencing factor of the low-frequency pressure fluctuation around the cavitating hydrofoil. Moreover, the NACA66 hydrofoil surface-pressure data are collected for dynamic mode decomposition to locate the hydrofoil surface noise sources. The alternate high and low amplitude regions in the mode results overlap highly with the cavitation transformation regions. The cavity transformation and pressure fluctuations are the main reason for the generation of periodic low-frequency noise source regions on the hydrofoil surface. Moreover, the corresponding frequencies of each order mode are linearly correlated with the cavitation shedding frequency of 5.70 Hz. Combined with the results of the multiple mode comparisons, it can be inferred that the hydrofoil suction surface under the cavitation effect will generate quasiperiodic waves starting from upstream and moving downstream.