To build a portable and sensitive method for monitoring the concentration of the flavonoid rutin, a new electrochemical sensing procedure was established. By using nitrogen-doped carbonized polymer dots (N-CPDs) anchoring few-layer black phosphorene (N-CPDs@FLBP) 0D-2D heterostructure and gold nanoparticles (AuNPs) as the modifiers, a carbon ionic liquid electrode and a screen-printed electrode (SPE) were used as the substrate electrodes to construct a conventional electrochemical sensor and a portable wireless intelligent electrochemical sensor, respectively. The electrochemical behavior of rutin on the fabricated electrochemical sensors was explored in detail, with the analytical performances investigated. Due to the electroactive groups of rutin, and the specific π-π stacking and cation–π interaction between the nanocomposite with rutin, the electrochemical responses of rutin were greatly enhanced on the AuNPs/N-CPDs@FLBP-modified electrodes. Under the optimal conditions, ultra-sensitive detection of rutin could be realized on AuNPs/N-CPDs@FLBP/SPE with the detection range of 1.0 nmol L−1 to 220.0 μmol L−1 and the detection limit of 0.33 nmol L−1 (S/N = 3). Finally, two kinds of sensors were applied to test the real samples with satisfactory results.