Chlorpyrifos (CPF) residues in food pose a serious threat to ecosystems and human health. Herein, we propose a three-dimensional folded paper-based microfluidic analysis device (3D-μPAD) based on multifunctional metal-organic frameworks, which can achieve rapid quantitative detection of CPF by fluorescence-colorimetric dual-mode readout. Upconversion nanomaterials were first coupled with a bimetal organic framework possessing peroxidase activity to create a fluorescence-quenched nanoprobe. After that, the 3D-μPAD was finished by loading the nanoprobe onto the paper-based detection zone and spraying it with a color-developing solution. With CPF present, the fluorescence intensity of the detection zone gradually recovers, the color changes from colorless to blue. This showed a good linear relationship with the concentration of CPF, and the limits of detection were 0.028 (fluorescence) and 0.043 (colorimetric) ng/mL, respectively. Moreover, the 3D-μPAD was well applied in detecting real samples with no significant difference compared with the high-performance liquid chromatography method. We believe it has huge potential for application in the on-site detection of food hazardous substance residues.