The in-situ synthesis of one-dimensional Co3O4@GO nanosorbent and its fabrication into the layers of Nylon-6 polymer have been introduced in the present study. The extraction performance of the prepared membrane was studied through using the prepared membrane for thin-film microextraction of two selected flavonoids (as the model compounds) from different kinds of juice and black tea. The extracted analytes (morin and quercetin) were quantified via high performance liquid chromatography-ultraviolet detection (HPLC-UV). The experimental design optimization strategy including Central Composite Design (CCD) was employed to optimize different TFME variables. The selected factors that were once thought to be effective on TFME were screened by Plackett–Burman Design before the optimization. The following figures of merit were obtained under the achieved optimized condition: the Linear Dynamic Ranges (LDRs): 5.0–500.0 μg L 1 and 5.0–200.0 μg L 1, Limits of Determination (LODs): 1.3 μg L 1 and 1.6 μg L 1, Limits of Quantification (LOQs): 4.3 μg L 1 and 5.1 μg L 1, the Relative Standard Deviations (RSDs) <4.7% (at two concentration levels of 5.0 and 200.0 μg L 1), Absolute Recovery (AR%): 73.0 and 64.0 and enrichment factors of 73.0 and 64.0 for morin and quercetin, respectively. The above-mentioned method was finally used to extract and determine morin and quercetin in natural orange juice, commercial orange juice, natural pear juice, commercial peach juice and black tea. The obtained results showed satisfactory relative recoveries from 90.0% to 98.0% and acceptable precisions (4.8% < RSD < 7.2%). Therefore, the presented method can be considered as an appropriate alternative to the conventional extraction methods in measuring trace amounts of flavonoids in real samples.