A novel fluorescence sensor of NR-β-CD@AuNPs was prepared for the trace detection of nitrite in quantities as low as 4.25 × 10−3 μg∙mL−1 in an aqueous medium. The fluorescence was due to the host-guest inclusion complexes between neutral red (NR) molecules and gold nanoparticles (AuNPs), which were modified by per-6-mercapto-beta-cyclodextrins (SH-β-CDs) as both a reducing agent and a stabilizer under microwave radiation. The color of the NR-β-CD@AuNPs changed in the presence of nitrite ions. A sensor was applied to the determination of trace nitrites in environmental water samples with satisfactory results.