Rutin, a natural flavonol glycoside, is widely present in plants and foods, such as black tea and wheat tea. The antioxidant and anti-inflammatory effects of flavonoids are well known. In this study, a new electrochemical rutin sensor was developed using multiwalled carbon nanotubes/aluminum-based metal–organic frameworks (MWCNT/CAU-1) (CAU−1, a type of Al-MOF) as the electrode modification material. The suspension of multiwalled carbon tubes was dropped on the surface of the GCE electrode to make MWCNT/GCEs, and CAU−1 was then attached to the electrode surface by electrodeposition. MWCNTs and CAU−1 were characterized using scanning electron microscopy (SEM) and X-ray photoelectron spectroscopy (XPS). Due to the synergistic effect of CAU−1 and MWCNT-COOH, the prepared sensor showed an ultrasensitive electrochemical response to rutin. Under optimized conditions, the sensor showed a linear relationship between 1.0 × 10−9~3.0 × 10−6 M with a detection limit of 6.7 × 10−10 M (S/N = 3). The sensor also showed satisfactory stability and accuracy in the detection of real samples.