A core-shell structure UiO-66-(OH)@UiO-66-NH (MOF@MOF) nanoparticle was synthesized through a simple hydrothermal method and employed as an adsorbent and laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS) matrix for the quantitative analysis of rhubarb anthraquinones (RAs). The properties of the materials were characterized by field emission scanning electron microscopy, transmission electron microscopy, energy-dispersive X-ray spectroscopy, X-ray powder diffraction, Fourier transform infrared spectroscopy, X-ray photoelectron spectroscopy, thermogravimetric analysis, and Brunauer-Emmett-Teller. The results indicate that MOF@MOF is regular octahedral structure with a size distribution of about 100 nm, having large BET specific surface area (920 m/g). Using the MOF@MOF as a matrix shows lower background interference, higher sensitivity, and better storage stability than that of traditional matrices. The MOF@MOF matrix exhibits excellent salt tolerance even under a NaCl concentration of 150 mM. Then, the enrichment conditions were optimized, and the adsorption time of 10 min, adsorption temperature of 40 °C and adsorbent amount of 100 μg were selected. In addition, the possible mechanism of MOF@MOF as an adsorbent and matrix was discussed. Finally, the MOF@MOF nanoparticle was employed as a matrix for the sensitive MALDI-TOF-MS analysis of RAs in spiked rabbit plasma, and the recoveries are in the range of 88.3–101.5% with RSD ≤9.9%. In short, the novel MOF@MOF matrix has demonstrated its potential in the analysis of small-molecule compounds in biological samples.