In this study, a novel fluorescent probe (graphene quantum dots functionalized d‐penicillamine [GQDs‐DPA]) was developed for the selective identification of Cu2+, V5+, and Fe3+ among 26 types of metal ions, which considerably quench the fluorescence intensity of GQD. So, GQDs‐DPA was applied as a simple fluorescent probe for facile metal ions recognition in standard solution. The proposed DPA‐GQD supported amino acids respond to Cu2+, V5+, and Fe3+, with high sensitivity. The intensity of the fluorescence histogram of this probe significantly diminished in exposure to metal ions such as Cu(II), V(V), and Fe(III). Moreover, a microfluidic paper‐based device (μPAD) was fabricated through a facile and cost‐effective protocol. Cu2+, V5+, and Fe3+ can be selectively recognized by GQDs‐DPA using μPAD by naked eye. Also, GQDs‐DPA exhibits a linear response for the detection of ions in concentrations ranging from 0.01 to 1 ppm, with a low limit of quantification of 0.01 ppm in standards samples. The boosted color uniformity, low instrumental needs of the stamp, and disposability of μPADs enable the application of the proposed device for commercial applications in environmental science and technology.