Abstract Seed size and weight are pivotal agronomic traits that link plant sexual reproduction to subsequent seedling establishment. These 2 seed characteristics are affected by embryo development and sugar filling. However, the molecular mechanisms controlling sugar translocation and the timing between early embryo development and subsequent seed filling in cucumber (Cucumis sativus L.) remain poorly understood. Here, we report that alkaline α-galactosidase 2 (CsAGA2) is expressed in the placental vascular bundles and funicular phloem, and its encoded protein is responsible for the hydrolysis of raffinose family oligosaccharides (RFOs). We demonstrate that FUSCA3 (CsFUS3) activates, while Auxin Response Factor 9 (CsARF9) represses, CsAGA2 expression. The CsFUS3–Sucrose Non-fermenting-1 (Snf1)-Related Protein Kinase 1α1 (CsSnRK1α1) interaction further enhances CsAGA2 expression, while CsARF9 recruits the TOPLESS (CsTPL) corepressor and further weakens CsAGA2 expression. Transgenic CsAGA2-RNAi (RNA interference), CsFUS3-RNAi, csfus3-crispr, and CsARF9-OE (overexpression) lines showed severe seed abortion rates, likely caused by reduced sugar supply during embryo development and seed filling. These results demonstrate the critical collaborative roles of these proteins in delivering sugars for seed development. Our findings reveal that CsAGA2 is an essential enzyme that is switched on by CsFUS3 to precisely regulate embryo development and provide the vast quantities of sugars needed for seed filling in cucumber. As the seeds mature, CsARF9 dampens CsAGA2 expression to gradually reduce the sugar supply to seeds. Therefore, our data suggest that the CsFUS3 and CsARF9 sequentially regulate embryo development and seed filling via CsAGA2-mediated RFO catabolism in cucumber. Our findings provide a new strategy for manipulating seed filling to increase yield in the breeding process of seed crops.