Chloroplast dynamic proteostasis modulates critical functions including photosynthesis. While the ubiquitin-proteasome system (UPS) degrades outer membrane proteins, mechanisms for intrachloroplastic protein degradation remain elusive. Here, we identify Arabidopsis Chloroplast-localized RING-type E3 ubiquitin ligases (CLRs) that directly govern photosystem homeostasis. These enzymes localize to intrachloroplastic membranes via non-canonical transport pathway. Sextuple clr-h mutant seedlings display light intensity-dependent lethality, whereas mature mutants exhibit enhanced photosynthetic performance and biomass under medium light, linked to preserved thylakoid integrity and reduced protein turnover. CLRs ubiquitinate photosynthetic complex subunits, promoting proteasomal degradation. This work reveals chloroplast-autonomous E3 ligases that directly balance photoprotection and photosynthetic efficiency through proteostasis modulation, expanding the spatial scope of UPS. Our findings establish intraorganellar ubiquitination as a key regulatory layer for environmental adaptation, offering strategies to improve crop photosynthesis.