A highly sensitive and selective electrochemical sensor based on a new molecularly imprinted polymer was proposed for the detection of estriol. Nitrogen-doped multi-walled carbon nanotube/graphene oxide nanoribbons (N-MWCNT/GONRs) were synthesized by the facile partially unzipping of N-MWCNTs with the help of microwave irradiation. The molecularly imprinted electrochemical sensor was fabricated by electrochemically polymerization of pyrrole onto N-MWCNT/GONR-modified Au electrode. Under the optimum condition, the sensor showed good response in the range of low concentrations from 0.1 μg·mL−1 to 20 μg·mL−1 with the detection limit (3σ, RSD ≤ 5%) of 2 ng·mL−1. Estradiol, diethylstilbestrol, oestrone bisphenol A, and ethinyloestradiol had negligible interference in the determination of estriol even when the concentration molar ratio reaches 50:1. The developed sensor had been applied to the reliable analysis of estriol in clinic samples and in real water samples with satisfactory results.