Paper-based optical sensors have emerged as a promising technology for pesticide detection and attracted extensive attention. However, in practical analytical applications, it may suffer from limited sensitivity with traditional signal amplification strategies. Here, we developed a novel mesoporous silica-modified paper-based sensor for a sensitive capture and analysis of the pesticide paraquat. Carboxylatopillar[5]arene was covalently introduced into the nanochannels for the rapid capture of target paraquat molecules due to the mass transfer confinement effect within nanopores. In addition, the large specific surface area of mesoporous silica enabled high-abundance immobilization of the capture agent and promoted its binding efficiency, which, in turn, contributed to improving the sensitivity. This work highlights the great potential of nanochannels as a development platform for sensitive paper-based sensors that can be used to develop new systems for the detection of paraquat and even other pesticides.