Plant photoperiodic growth is coordinated by interactions between circadian clock and light signaling networks. How post‐translational modifications of clock proteins affect these interactions to mediate rhythmic growth remains unclear. Here, we identify five phosphorylation sites in the Arabidopsis core clock protein TIMING OF CAB EXPRESSION 1 (TOC1) which when mutated to alanine eliminate detectable phosphorylation. The TOC1 phospho‐mutant fails to fully rescue the clock, growth, and flowering phenotypes of the toc1 mutant. Further, the TOC1 phospho‐mutant shows advanced phase, a faster degradation rate, reduced interactions with PHYTOCHROME‐INTERACTING FACTOR 3 (PIF3) and HISTONE DEACETYLASE 15 (HDA15), and poor binding at pre‐dawn hypocotyl growth‐related genes (PHGs), leading to a net de‐repression of hypocotyl growth. NUCLEAR FACTOR Y subunits B and C (NF‐YB/C) stabilize TOC1 at target promoters, and this novel trimeric complex (NF‐TOC1) acts as a transcriptional co‐repressor with HDA15 to inhibit PIF‐mediated hypocotyl elongation. Collectively, we identify a molecular mechanism suggesting how phosphorylation of TOC1 alters its phase, stability, and physical interactions with co‐regulators to precisely phase PHG expression to control photoperiodic hypocotyl growth. SYNOPSIS: Photoperiodic growth of plants is coordinated by an interplay between light signaling and circadian clock. This study reports that phosphorylation of a key Arabidopsis clock protein, TOC1, is essential for its function in repressing hypocotyl growth in the dark. Alanine substitution of five newly discovered phosphosites in the N‐terminus of TOC1 phenocopies clock and developmental defects of the toc1 mutant.TOC1 phospho‐mutations alter the protein expression profile, diminishing TOC1 stability, chromatin binding and interaction with PIF3.TOC1 forms a trimeric complex with NF‐YB/C and recruits HDA15 to repress pre‐dawn‐phased hypocotyl growth‐related genes at night.TOC1 phospho‐mutations diminish interactions with NF‐YB/C, decreasing chromatin residence of TOC1. [ABSTRACT FROM AUTHOR]