The transition to flowering is a major developmental switch in flowering plants. The nuclear RNA-binding protein FCA responds to seasonal signals and abscisic acid (ABA), which can control the flowering time via ambient temperature and autonomous pathways. Citrus FCA ortholog (PtFCA) has been isolated and characterized from precocious trifoliate orange (Poncirus trifoliata L. Raf). Three alternatively spliced transcripts of PtFCA (PtFCA1, PtFCA2, and PtFCA3) were isolated. The expression pattern of PtFCA indicated that it may be involved in phase transition in precocious trifoliate orange. A functional complementation experiment of PtFCA indicated that PtFCA1 partially rescued the late-flowering phenotype of the fca-1 mutant. There was no influence on flowering time of transgenic Arabidopsis by PtFCA3 as compared with PtFCA2, which exhibits delayed flowering time in a fca-1 background. Meanwhile, these three transcripts also showed different abilities to regulate root development in the fca-1 background. The study of protein–protein interactions suggested that PtFCA may form higher order complexes with PtFY and PtNF-YA7 to regulate timing of the transition from the vegetative to reproductive phase in precocious trifoliate orange. ABA and ambient temperature treatments changed the expression of PtFCA and interaction protein. These findings reveal that PtFCA may play important roles in flowering time and root development of precocious trifoliate orange through the formation of multiple protein complexes.