Herein, a paper-based fluorescence sensor based on the metal-organic frameworks capped with aptamer and molecular imprinted polymer (MOF-Apt@MIP) was designed for malachite green (MG) and realized sensitive detection by using digital image colorimetry with the aid of smartphone. The green fluorescence terbium MOF-76 was prepared and used as a carrier to conjugate with MG specific aptamer. MG, as template molecule, was subsequently added into MOF-Apt to generate MIP layer under the action of co-polymerization process. With the addition of MG, the fluorescence of MOF-Apt@MIP was quenched because MG was synergistically bound with aptamer and MIP and induced photo-induced electron transfer (PET) effect. Then, the obtained MOF-Apt@MIP probe was applied to a circle pattern paper and measured by a smartphone, in which color recognition software was installed to read out the RGB values of the acquired images. The detection limit for paper-based detection was 0.1 ng/mL. This point of care testing (POCT) method was applied to detect MG in fish and water samples with recoveries in 94.0–105.6 %. This method endows synergistic binding effect of aptamer and MIP, enhancing the detection sensitivity and specificity, and the paper-based detection with smartphone facilitate the on-site monitoring. It is expected that this sensor will be of great significance for the detection and monitoring of illegal additive in food stuffs.