We synthesized a novel cage-ladder-structure, phosphorus-containing polyhedral oligomeric silsesquinoxane (CLEP-DOPO-POSS) via the hydrolytic condensation of 9,10-dihydro-9-oxa-10-phosphaphenanthrene-10-oxide (DOPO)-vinyl trimethoxysilane (VTMS) with 2-(3,4-epoxycyclohexyl) ethyl trimethoxysilane and then incorporated it into epoxy resins (EPs) in different ratios with thermal curing technology. The structure of CLEP-DOPO-POSS was confirmed by Fourier transform infrared spectroscopy, NMR spectroscopy ( 1 H-NMR and 29 Si-NMR), matrix-assisted laser desorption ionization time-of-flight, and X-ray diffraction. The thermal stability, mechanical properties and flame retardancy effect of CLEP-DOPO-POSS on EP were comprehensively evaluated via thermogravimetric analysis (TGA), dynamic mechanical analysis, universal tensile testing, limiting oxygen index (LOI) measurement, UL-94 testing, and cone calorimetry. The flame-retardant mechanism of the EP modified with CLEP-DOPO-POSS was investigated by TGA-IR, TGA-mass spectrometry, and scanning electron microscopy. The experimental results show that CLEP-DOPO-POSS was homogeneously dispersed in the EP matrix. The LOI value reached 31.9, and the UL-94 grade passed V-0 with the presence of only 0.28% P (2.91 phr CLEP-DOPO-POSS). In addition, the EP composite containing CLEP-DOPO-POSS exhibited a better thermal stability and mechanical properties. The flameretardant mechanism was attributed to the quenching effect of the phosphorus-containing free radicals and the formation of phosphorusand silicon-containing char layers in the condensed phase.