Autophagy is a highly conserved and regulated catabolic process involved in the degradation of protein aggregates, and it plays critical roles in eukaryotes. In plants, autophagy has been well studied in stress responses. Although multiple molecular processes can induce or suppress autophagy, the mechanism of its regulation by phytohormones is poorly understood. Brassinosteroids (BRs) are steroid phytohormones that play crucial roles in plant response to stresses. In present study, we investigate the role of BRs in NBR1-dependent selective autophagy in response to chilling stress in tomato. BRs and their signaling element BZR1 can induce autophagy and protein accumulation of its selective receptor NBR1 in tomato under chilling stress. Cold increased the stability of BZR1, which was promoted by BRs. Cold- and BR-induced BZR1 stability activated the transcription of several ATGs and NBR1 genes by directly binding to the promoters of those genes, which resulted in the formation of selective autophagy. Furthermore, silencing of these ATGs or NBR1 genes resulted in the decreased accumulation of several functional proteins and the increased accumulation of ubiquitinated proteins, subsequently compromised BR-induced cold tolerance. These results strongly suggest that BRs regulate NBR1-dependent selective autophagy by BZR1-dependent manner in response to chilling stress in tomato.