The electrocatalytic nitrate reduction reaction (NitRR) represents a promising approach toward achieving economically and environmentally sustainable ammonia. However, it remains a challenge to regulate the size effect of electrocatalysts to optimize the catalytic activity and ammonia selectivity. Herein, the Cu-based catalysts were tailored at the atomic level to exhibit a size gradient ranging from single-atom catalysts (SACs, 0.15–0.35 nm) to single-cluster catalysts (SCCs, 1.0–2.8 nm) and nanoparticles (NPs, 20–30 nm), with the aim of studying the size effect for the NO₃⁻-to-NH₃ reduction reaction. Especially, the Cu SCCs exhibit enhanced metal–substrate and metal–metal interactions by taking advantageous features of Cu SACs and Cu NPs. Thus, Cu SCCs achieve exceptional electrocatalytic performance for the NitRR with a maximum Faradaic efficiency of ca. 96% and the largest yield rate of ca. 1.99 mg ${}_{{\mathrm{N}\mathrm{H}}_3}$·h⁻¹·cm⁻² at −0.5 V vs. reversible hydrogen electrode (RHE). The theoretical calculation further reveals the size effect and coordination environment on the high catalytic activity and selectivity for the NitRR. This work provides a promising various size-controlled design strategy for aerogel-based catalysts effectively applied in various electrocatalytic reactions.