This study explores the influence of surface microstructures, on controlling cloud cavitation dynamics over a three-dimensional Clark Y hydrofoil. The investigation focuses on the effects of rows of semi-spherical microstructures, strategically placed at three different locations on the hydrofoil's suction side. The study utilizes the Large Eddy Simulation (LES) approach to investigate the influence of these configurations on the cloud cavitation lifecycle, focusing on aspects such as cloud shedding frequency, hydrofoil efficiency, cavitation volume, and overall unsteadiness. The Reynolds number is considered to be 7 x 105 and the angle of attack of the hydrofoil is fixed at 8 degrees. The results showed that placing the microstructures near the leading edge prolonged the sheet cavity and reduced the cloud cavitation shedding frequency by 5 %. However, this configuration also resulted in an 11.45 % decrease in the lift-to-drag ratio. Positioning semi-spherical microstructures along the mid-chord line resulted in a 4 % increase in cloud cavitation shedding frequency and a 5 % reduction in the lift- to-drag ratio. In contrast, implementing the semi-spherical surface microstructures near the trailing edge influenced the re-entrant jet and local pressure distribution, breaking large cavities into smaller ones. This naturally increased the frequency of cavity shedding by 19.4 % while also increasing the lift-to-drag ratio by approximately 2.5 %. The study also analyzes surface-vortex-cavitation interaction using the vorticity transport equation, finding that microstructures enhance vortex stretching while reducing vortex dilatation and baroclinic torque terms. Overall, the findings suggest that microstructures can stabilize cloud cavitation, leading to a more uniform pressure distribution and smoother flow over the hydrofoil.