Metal-organic frameworks (MOFs) based composites with different structure-activity relationships have been widely used in the field of organic pollutant adsorption and extraction. Here, two MOF-on-MOF composites with different structures (yolk-shell and core-shell) from homologous sources were prepared by a simple in-situ growth synthesis method and structural regulation. In order to verify the effect of composite structure on the extraction capacity, the adsorption performance of the yolk-shell structure (YS–NH2-UiO-66@CoZn-ZIF) and the core-shell structured (NH2-UiO-66@CoZn-ZIF) material were compared by using them as coating material of direct immersion solid-phase microextraction (DI-SPME) to enrich six pesticides in five matrices. The results showed that because of the unique hollow hierarchical structure, high specific surface area (930.68 m2 g−1), abundant and open active sites, and synergistic and complementary adsorption forces, YS-NH2-UiO-66@CoZn-ZIF composites had the maximum adsorption amount of 36.01–66.31 mg g−1 under the same experiment condition, which was 6.81%–34.26 % higher than that of NH2-UiO-66@CoZn-ZIF. In addition, the adsorption mechanism of the prepared materials was verified and elaborated through theoretical simulations and material characterization. Under the optimized conditions, the YS-NH2-UiO-66@CoZn-ZIF-coated SPME-HPLC-UV method had a wide linear range (0.241–500 μg L−1), a good linear correlation coefficient (R2 > 0.9988), a low detection limits (0.072–0.567 μg L−1, S/N = 3) and low quantification limits (0.241–1.891 μg L−1, S/N = 10). The relative standard deviations of individual fibers and different batches of fibers were 0.47–6.20 % and 0.22–2.48 %, respectively, and individual fibers could be recycled more than 104 times. This work provided a good synthetic route and comparative ideas for exploring the in-situ growth synthesis of yolk-shell composites with reasonable structure-activity relationships.