Removal of trace chlorobutane (CB) isomers is highly desired to produce high grade 1-chlorobutane (1-CB) and 2-chlorobutane (2-CB). Here, we report that nonporous adaptive crystals (NACs) of perethylated pillar[S]arene (EtPS) and pillar[6]arene (EtP6) effectively remove trace CB isomers. EtPS NACs can remove trace 1-CB (2%) from 2-CB to improve its purity from 98.0% to 99.9%, while EtP6 NACs can remove trace 2-CB from 1-CB to improve its purity from 98.0% to 99.9%. The adsorption of trace CB isomers results in the formation of new CB-loaded crystal structures, whose thermostability is higher than their corresponding isomer-loaded structures. This determines the selectivity of NACs toward the trace CB isomers. Reversible transformations between nonporous guest-free and guest-loaded structures make EtPS and EtP6 highly recyclable.