Abstract The mechanical properties and deformation behavior of CoCrNiAl medium entropy alloy (MEA) subjected to indentation by an indenter tooltip on the substrate are explored using molecular dynamics (MD) simulation. The study investigates the effects of alloy compositions, temperature variations, and ultra vibration (UV) on parameters, such as total force, shear strain, shear stress, hardness, reduced modulus, substrate temperature, phase transformation, dislocation length, and elastic recovery. The findings indicate that higher alloy compositions result in increased total force, hardness, and reduced modulus, with Ni-rich compositions demonstrating superior mechanical strength. Conversely, increasing alloy compositions lead to reduced von Mises stress (VMS), phase transformation, dislocation distribution, and dislocation length due to the larger atomic size of Ni compared to other primary elements. At elevated substrate temperatures, atoms exhibit larger vibration amplitudes and interatomic separations, leading to weaker atomic bonding and decreased contact force, rendering the substrate softer at higher temperatures. Additionally, higher initial substrate temperatures enhance atom kinetic energy and thermal vibrations, leading to reduced material hardness and increased VMS levels. Increasing vibration frequency enlarges the indentation area on the substrate’s surface, concentrating shear strain and VMS with vibration frequency. Higher vibration amplitude and frequency amplify force, shear strain, VMS, substrate temperature, and dislocation distribution. Conversely, lower vibration amplitude and frequency result in a smaller average elastic recovery ratio. Moreover, increased amplitude and frequency values yield an amorphous-dominated indentation region and increased proportions of hexagonal close-packed and body-centered cubic structures. Furthermore, this study also takes into account the evaluation of a material’s ability to recover elastically during the indentation process, which is a fundamental material property.