The adsorptions of CO and CO2 on pristine and transition metal-doped graphene nanoflakes (GNFs) were theoretically investigated using the density functional theory. Doping of a series of 3d transition metals (TM = Sc, Ti, V, Cr, Mn, Fe, Co, Ni, Cu, or Zn) to pristine GNF can significantly enhance the adsorption abilities of GNF, leading to a stronger interaction between gas molecule and GNF. Among all transition metal-doped GNFs, Cr-doped GNF shows the highest adsorption strength toward both of CO and CO2 molecules. Calculated electronic properties for studied systems indicate that TM-doped GNFs present high sensitivity to CO and CO2 molecules. In addition, the adsorptions of the CO and CO2 molecules on TM-doped GNF are influenced on the electronic conductance of the TM-doped GNF. The results of this study may serve to enhance the application of effective CO and CO2 gas storage and sensor to preserve the environment based on GNF.