A preparation method involving the combination of high-pressure homogenization and ultrasound (HPH-US) techniques was employed to produce starch nanocrystals (NCs) from three botanical starch sources: chestnut, corn starch, and potato starch. The optimal conditions, determined using response surface methodology, consisted of a homogenization pressure of 60 MPa and ultrasound at 280 W for 30 min. The utilization of dynamic light scattering (DLS) and transmission electron microscopy (TEM) unveiled that the resulting starch particles exhibited nanometric dimensions ranging from 135.36 to 203.47 nm. The mechanical forces generated by the HPH-US treatment significantly enhanced the physicochemical properties of the starch NCs, leading to a partial disruption of the crystalline structure. Moreover, the potential application of the synthesized starch NCs as fat replacers (FRs) was investigated. As the degree of substitution increased, notable improvements were observed in the hardness and viscosity of ice cream, accompanied by a reduction in the melting rate. The overall sensory evaluation indicated that corn starch NCs held substantial promise as a viable alternative FR for enhancing the quality of ice cream.