In this study, amino-modified micro-mesoporous silica (NH2-MMS) with hierarchical pores was prepared by modifying micro-mesoporous silica ZSM-5 with 3-aminopropyltriethoxysilane and used as an adsorbent in solid-phase extraction to analyze free fatty acids (FFAs) in krill oil during storage for an initial time. The Brunner Emmet Teller adsorption experiment and Fourier transform infrared spectroscopy demonstrate that NH2-MMS, with a hierarchical pore structure, was successfully synthesized. The adsorption experiments, especially static adsorption, indicate that the absorption ability of the prepared NH2-MMS, with a hierarchical pore structure, toward FFAs was better than that of traditional amino-modified mesoporous silica (SBA-15) with a mesoporous structure at all temperature and concentrations. Fairly low limits of detection (0.06–0.15 μg g−1), acceptable recoveries (85.16–94.31%), and precision (0.08–5.26%) were attained under ideal circumstances. Moreover, NH2-MMS has the advantages of easy preparation and being environmentally friendly. As a result, this method offers an alternative to the current method for determining FFAs in different kinds of oil specimens.