Selective catalytic hydrogenation has wide applications in both petrochemical and fine chemical industries, however, it remains challenging when two or multiple functional groups coexist in the substrate. To tackle this challenge, the active site isolation strategy has been proved effective, and various approaches to the site isolation have been developed. In this review, we have summarized these approaches, including adsorption/grafting of N/S-containing organic molecules on the metal surface, partial covering of active metal surface by metal oxides either via doping or through strong metal-support interaction, confinement of active metal nanoparticles in micro- or mesopores of the supports, formation of bimetallic alloys or intermetallics or core@shell structures with a relatively inert metal (IB and IIB) or nonmetal element (B, C, S, etc.), and construction of single-atom catalysts on reducible oxides or inert metals. Both advantages and disadvantages of each approach toward the site isolation have been discussed for three types of chemoselective hydrogenation reactions, including alkynes/dienes to monoenes, alpha,beta-unsaturated aldehydes/ketones to the unsaturated alcohols, and substituted nitroarenes to the corresponding anilines. The key factors affecting the catalytic activity/selectivity, in particular, the geometric and electronic structure of the active sites, are discussed with the aim to extract fundamental principles for the development of efficient and selective catalysts in hydrogenation as well as other transformations.