Alternative splicing of primary gene transcripts provides eukaryotic cells, with a critical scheme for enriching transcriptome and proteome diversity. Here we report that alternative splicing of the Arabidopsis INDERMINATE DOMAIN 14 (IDD14) transcription factor gene generates a competitive inhibitor in regulating starch metabolism. An alternatively spliced IDD14 form (IDD14β), which is produced predominantly under cold conditions, lacks functional DNA-binding domain but is able to form heterodimers with the functional IDD14 form (IDD14α). IDD14α-IDD14β heterodimers have reduced binding activity to the promoter of Qua-Quine Starch (QQS) gene that regulates starch accumulation. Transgenic Arabidopsis plants overproducing IDD14α (35S:IDD14α) exhibited retarded growth with pale green leaves as appeared on QQS-overexpressing plants. Notably, IDD14β overproduction rescued the 35S:IDD14α phenotypes. We propose that alternative splicing of the IDD14 gene generates a self-controlled regulatory loop that may modulate starch accumulation in response to cold.