An ultrasensitive and rapid sequential injection analysis (SIA) based on real-time PCR (SIA-rt-PCR) assay was developed by using different nanoparticles for the detection of small molecule chemicals residues. Gold (Au) nanoparticle, conjugated with goat anti-rabbit IgG and duplex strand DNA (dsDNA), was used as a substitute for chemiluminescent probes in an SIA system. By indirect competitive immunoreactions in the SIA system, the gold nanoparticles were attached to antigens which were immobilized by superparamagnetic nanoparticles (SMNPs). The dsDNA on the gold nanoparticles was dehybridized and then the single-stranded DNA (ssDNA) was collected and quantified with rt-PCR, which showed a rather low linearity range from 2.5 attomol L(-1) (aM) to 250 femtomol L(-1) (fM) and the LOD was 1.4 aM. This method, which is rapid, automated and capable of high-throughput, was used to detect methyl-3-quinoxaline-2-carboxylic acid (MQCA) residues in real samples. The analytical results had a coefficient of variation of less than 15% and the recovery was 89-108%.