A sensitive nanopipette sensor is established through a unique design of host–guest recognition, which could be further enhanced by the introduction of gold nanoparticles (Au NPs). Generally, the nanopipette is conjugated with caboxylatopillar[5]arenes (CP[5]) or carboxylated leaning pillar[6]arene (CLP[6]) to generate recognition sites. After the addition of pesticide molecules, they would be captured by CP[5] (or CLP[6]), resulting in a significant electronegativity change on the nanopipette’s inner surface, which could be determined by the ionic current change. The CP[5]-modified nanopipette exhibited reliable selectivity for paraquat, while the CLP[6]-modified nanopipette showed an ability of detection for both paraquat and diquat. The addition of Au NPs improved the selectivity and sensitivity of the CP[5]-Au NP-modified nanopipette for paraquat sensing. After optimization by lowering the size of the Au NPs, CP[5]-Au NPs (3 nm)-modified nanopipettes achieved lower detection limits of 0.034 nM for paraquat. Furthermore, in real sample analysis, this sensor demonstrates exceptional sensitivity and selectivity. This study provides a new strategy to develop nanopipette sensors for practical small molecule detection. Graphical abstract: The gold nanoparticles enhanced quartz nanopipette sensor based on host-guest interaction was firstly established, which could achieve an excellent limit of detection of 3.4 × 10-11 mol/L for paraquat. [Figure not available: see fulltext.].