Exact assay of matrix metalloproteinase 9 (MMP9) has attracted considerable attentions for the clinical diagnosis of disease in early stage. In this report, we covalently engineer a fluorescein isothiocyanate-labeled peptide (Pep-FITC) linker containing the specific cleavage substrate of MMP9 onto the surface of hydrothermally reduced nano-graphene oxide (nrGO) to develop a FRETbased nrGO-Pep-FITC nanoprobe for ultrasensitive detection of MMP9. Upon cleavage of the Pep-FITC at the amide bond between Ser and Leu by MMP9, FITC was separated from nrGO, and fluorescence recovery of FITC was proportional to the MMP9 concentration within 0.01-0.06 nM and 0.06-0.15 nM ranges, respectively, in an aqueous solution, exhibiting 0.83 pM of detection limit. This nanoprobe is stable under borate buffer (pH = 7.4) with bovine serum albumin or 0.1% surfactant Triton 100 or Tween 20, and has good specificity for MMP9 detection, which is meaningful for MMP9-related clinical and bioanalytical applications.