A core-shell material (UiO@TapbTp) has been developed as an adsorbent and matrix to detect nonsteroidal anti-inflammatory drugs (NSAIDS) by matrix laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) in complex samples. The hybrid material is prepared by growing covalent organic framework (COF, TapbTp) layers in situ on an amino-modified metal-organic framework (MOF, UiO-66-NH2). The combination of the MOF and COF overcomes their individual shortcomings and integrates both of their advantages. Compared with the bare COF and MOF, the core-shell composite exhibits improved enrichment ability and matrix performance. With the help of pre-enrichment under optimized conditions, the limits of detection (LODs) for ketoprofen, naproxen, and aspirin are reduced by nearly 1000 times, with values of 0.001 mg L−1, 0.010 mg L−1, and 0.001 mg L−1, respectively, and the relative standard deviations (RSDs) are all below 12.35%. The good recoveries (84.8–118%) in (spiked) saliva and environmental water sample further verify the applicability of the method in complex samples.