In this work, multi‐layer Ti3C2 – carbon nanotubes – gold nanoparticles (Ti3C2‐CNTs‐Au) and cyclodextrin metal‐organic framework – carbon nanotubes (CD‐MOF‐CNTs) have been prepared by in situ growth method and used to construct the ultra‐sensitive rutin electrochemical sensor for the first time. Among them, the large number of metal active sites of Ti3C2, the high electron transfer efficiency of CNTS, and the good catalytic properties of AuNPs significantly enhance the electrochemical properties of the composite carbon nanomaterials. Interestingly, CD‐MOF has a unique host–guest recognition and a large number of cavities, molecular gaps, and surface reactive groups, which gives the composite outstanding accumulation properties and selectivity for rutin. Under the optimized conditions, the constructed novel sensor has satisfactory detection performance for rutin in the range of 2 × 10−9 to 8 × 10−7 M with a limit of detection of 6.5 × 10−10 M. In addition, the sensor exhibits amazing anti‐interference performance against rutin in some flavonoid compounds and can be used to test natural plant samples (buckwheat, Cymbopogon distans, and flos sophorae immaturus). This work has promising applications in the field of environmental and food analysis, and exploring new directions for the application of Mxene‐based composites.