A piperazinylalkylisoxazole library containing 86 compounds was constructed and evaluated for the binding affinities to dopamine (D3) and serotonin (5-HT2A/2C) receptor to develop antipsychotics. Dopamine antagonists (DA) showing selectivity for D3 receptor over the D2 receptor, serotonin antagonists (SA), and serotonin-dopamine dual antagonists (SDA) were identified based on their binding affinity and selectivity. The analogues were divided into three groups of 7 DAs (D3), 33 SAs (5-HT2A/2C), and 46 SDAs (D3 and 5-HT2A/2C). A classification model was generated for identifying structural characteristics of those antagonists with different affinity profiles. On the basis of the results from our previous study, we conducted the generation of the decision trees by the recursive-partitioning (RP) method using Cerius2 2D descriptors, and identified and interpreted the descriptors that discriminate in-house antipsychotic compounds.