Dispersive-micro solid phase extraction (d-µSPE) has gained increasing attention due to its convenience, effectiveness, and flexibility for sorbent selection. Among a various selection of materials, magnetic carbon nanotubes (Mag-CNTs) is a promising d-µSPE sorbent with excellent separation efficiency in addition to its high surface area and adsorption capability. In this work, two different surface-modified Mag-CNTs, Mag-CNTs-COOH and Mag-CNTs-SO3H, were developed to facilitate d-µSPE (Mag-CNTs/d-µSPE). The cyanide metabolite, 2-aminothiazoline-4-carboxylic acid (ATCA), was selected to evaluate their extraction performance using gas chromatography–mass spectrometry (GC–MS) analysis. The Mag-CNTs-COOH enabled a one-step derivatization/desorption approach in the workflow; therefore, a better overall performance was achieved. Compared to the Mag-CNTs-SO3H/d-µSPE and SPE workflow, the one-step desorption/derivatization approach improved the overall extraction efficiency and reduced solvent consumption and waste production. Both Mag-CNTs/d-µSPE workflows were validated according to ANSI/ASB 036 guidelines and showed excellent analytical performances. The limit of detection (LOD) and limit of quantitation (LOQ) of ATCA in synthetic urine were 5 and 10 ng/mL, respectively, and that in bovine blood were achieved at 10 and 60 ng/mL. The SPE method’s LOD and LOQ were also determined at 1 and 25 ng/mL in bovine blood samples. The Mag-CNTs/d-µSPE methods demonstrated great potential to extract polar and ionic metabolites from biological matrices. The extraction processes of ATCA described in this work can provide an easier-to-adopt procedure for potential routine forensic testing of the stable biomarker in cyanide poisoning cases, particularly for those cases where the cyanide detection window has passed.