Abscisic acid (ABA) controls many physiological processes and mediates adaptive responses to abiotic stresses. The ABA signaling mechanisms for abscisic acid receptors PYR/PYL/RCAR (PYLs) were reported. However, it remains unclear whether the molecular mechanisms are suitable for other PYLs. Here, complex structures of PYL3 with (+)-ABA, pyrabactin and HAB1 are reported. An unexpected trans-homodimer intermediate observed in the crystal is confirmed in solution. ABA-bound PYL3 greatly promotes the generation of monomeric PYL3, which can excessively increase the efficiency of inhibiting PP2Cs. Structure-guided biochemical experiments show that Ser195 accounts for the key intermediate. Interestingly, pyrabactin binds to PYL3 in a distinct nonproductive mode with gate closure, which sheds light on the design of agonists and antagonists for abscisic acid receptors. According to different conformations of ligand-bound PYLs, the PYLs family can be divided into three subclasses, among which the trans-dimeric subclass, represented by PYL3, reveals a distinct regulatory mechanism.