Auxin plays a central role in numerous developmental processes throughout the plant lifespan. Despite its well-established roles in plant growth, how auxin determines seed size and the molecular mechanism that links auxin signaling and seed size regulators still remain unclear. Here, we report that the auxin co-receptor TMK1 acts maternally to regulate seed size and mediates auxin-promoted seed growth in Arabidopsis. TMK1 interacts with and phosphorylates the peptidase DA1, a key negative regulator of seed size, resulting in the destabilization of DA1. This process is stimulated by auxin, which not only promotes DA1 phosphorylation but also facilitates the accumulation of its target, the ubiquitin-specific protease UBP15, through TMK1. Genetic analyses further support that TMK1, DA1, and UBP15 act in the same pathway to control seed size. Thus, our findings reveal a novel mechanism by which auxin signaling controls seed size through TMK1-dependent phosphorylation and destabilization of DA1 in Arabidopsis, offering a perspective for seed size improvement in crops.