The preparation and application of inorganic-organic hybrid nanomaterials is a hot research topic at present. Herein, we combined Zn-Al layered double hydroxide (Zn-Al LDH) with mesoporous polydopamine (MPDA) to prepare two integrated Zn-Al LDH@MPDA nanocomposites under the modification of linker (1,3,5-benzoyl chloride (TMC) or (3-aminopropyl) trimethoxysilane (APTMS)), namely Composite T (modified by TMC) and Composite A (modified by APTMS), which were then evaluated for dye adsorption, adriamycin hydrochloride (DOX) loading, photothermal conversion experiment, and antibacterial test. The characterization results showed that MPDA can be successfully loaded on Zn-Al LDH with the modification of the two linkers, but the specific surface area, pore-volume, average pore size, and electronegativity of Composite T were all higher than those of composite A, thus being more advantageous in adsorption of cationic dye. Composite T possesses a high loading capacity for DOX, whose loading efficiency and encapsulation efficiency are 478.3% and 95.7%, respectively. In addition, Composite T also shows a high photothermal conversion efficiency of 27.9%. Furthermore, Composite T exhibits excellent antibacterial activity against Escherichia coli (E. coli) and Staphylococus aureus (S. aureus). Therefore, the designed Zn-Al LDH@MPDA nanocomposites would be a promising candidate for a myriad of industrial application fields.