Copper (Cu) and cadmium (Cd) are toxic to plants at high levels. The current situation that many crops are growing on the farmlands with Cu or Cd contamination leads to a big threat to food safety. Based on the small RNA (sRNA) sequencing data, hundreds of the sRNAs responsive to excessive Cu or Cd treatment were extracted. Degradome sequencing data enabled us to identify the targets of the metal stress-responsive sRNAs. According to our results, many sRNAs are responsive to both treatments, indicating the interactions between the Cu and Cd signals. A total of 151 sRNAs are DCL (Dicer-like) 1-dependent, and 156 sRNAs are DCL2/3/4-dependent. Some sRNAs found their loci on rRNAs or tRNAs, and a total of 12 sRNAs were potentially originated from the TAS transcripts. Functional analysis of the regulatory network showed that some of the sRNA--target pairs played a potential role in plant reproduction, and some pairs were possibly implicated in hormone--stress signal interactions. Our study could inspire the development of an efficient approach, possibly through the manipulation of the sRNA-guided regulatory pathways, to improve the stress tolerance or reduce the toxic metal accumulation levels of plants.