Trace detection of carbendazim (CBZ), a worldwide used pesticide, in crops and foods is important and urgent to reduce risks to human health. Herein, newly red-emissive carbon dots (R-CDs) based fluorescent and smartphone-integrated paper sensors were developed for highly-selective, and -sensitive rapid sensing of CBZ. R-CDs were synthesized from citric acid and urea via a DMF solvothermal method, which showed excellent analytical performance due to abundant carboxyl groups on the surface and long emission wavelength to avoid autofluorescence interference of matrix. According to the red fluorescence quenching by CBZ via π-π interaction and photoinduced electron-transfer effect, the newly fluorescent nano sensor could realize CBZ sensing within 3 min with high selectivity out of the other six interfering pesticides, as well as fascinating sensitivity with an ultralow detection limit of 3.5 ng/mL. The practicable application in the spiked medicinal Lotus seeds samples exhibited satisfactory recoveries of 95.5%-108.3%. The portable paper-based sensor fabricated by depositing R-CDs on the filter paper enabled quantitative readout of test strip results assisted with a smartphone, providing a rapid on-site tool for CBZ detection in medicinal foods. This is the first report of a novel, sensitive, and portable R-CDs based sensing platform for simple, cost-effective, and rapid on-site detection of CBZ in the field of food safety with great application potential.