In this study, a chalcone-branched polyimide (CB-PI) was synthesized by the Steglich esterification reaction for selective recognition of the toxic peptide melittin (MEL). MEL was immobilized on a nanopatterned poly(dimethylsiloxane) (PDMS) mold using a conventional surface modification technique to increase binding sites. A stripe-nanopatterned thin CB-PI film was formed on a quartz crystal (QC) substrate by simultaneously performing microcontact printing and ultraviolet (UV) light dimerization using a MEL-immobilized mold. The surface morphology changes and dimensions of the molecularly imprinted polymer (MIP) films with stripe nanopatterns (S-MIP) were analyzed using scanning electron microscopy (SEM) and atomic force microscopy (AFM). The sensing signals (Δf and Q e ) of the S-MIP sensor were investigated upon adsorption in a 100-μL dilute plasma solution containing 30 μg/ mL MEL, and its reproducibility, reuse, stability, and durability were investigated. The S-MIP sensor showed high sensitivity (5.49 mL/mg) and coefficient of determination (R 2 = 0.999), and the detection limit (LOD) and the quantification limit (LOQ) were determined as 0.3 and 1.1 μg/mL, respectively. In addition, the selectivity coefficients (k*) calculated from the selectivity tests were 2.7−5.7, 2.1−4.3, and 2.8− 4.6 for bovine serum albumin (BSA), immunoglobulin G (IgG), and apamin (APA), respectively. Our results indicate that the nanopatterned MIP sensors based on CB-PI demonstrate great potential as a sensing tool for the quantitative analysis of biomolecules.