This study introduces an advanced electrochemical sensor fabricated by immobilizing nitrogen-doped malic acid carbon quantum dots (N-MCQDs) onto a glassy carbon electrode (GCE) via microwave-assisted synthesis and electrodeposition. The N-MCQDs were comprehensively characterized using high-resolution transmission electron microscopy (HRTEM), X-ray diffraction (XRD), Fourier transform infrared spectroscopy (FTIR), X-ray photoelectron spectroscopy (XPS), Raman spectroscopy, and atomic force microscopy (AFM), confirming their successful synthesis and uniform distribution on the GCE surface. The N-MCQDs-modified GCE electrode (N-MCQDs/GCE) sensor displayed a remarkable linear detection range of 1–500 μM for hydroquinone (HQ) and 1–200 μM for catechol (CC), with ultra-low detection limits of 0.18 μM for HQ and 0.13 μM for CC. It also exhibits commendable stability, interference resistance, and the capability to accurately measure in complex real sample. These superior characteristics were attributed to the enhanced electrical conductivity and increased active sites due to nitrogen doping. This study not only broadens the application spectrum of carbon quantum dots but also offers a novel perspective for the design of high-performance electrochemical sensors for environmental analysis.