Phenylphosphonyl dichloride (BPOD) and 3-aminopropyltriethoxysilane (APTES) were used to prepare phosphorus-nitrogen hexaethoxysilane (BPTES). BPTES was then used for cross-linking and curing hydroxyl-terminated room-temperature vulcanized (RTV) silicone rubber, providing intrinsic flame retardancy. In addition, halloysite (HNTs) is a kind of tubular silicate, taking advantage of its large aspect ratio, HNTs were used as a template to load ZIF67 on the surface of halloysite to obtain HNTs@ZIF tubular filler. It was added to the above system as a reinforcing and flame-retardant filler by physical blending, and the RTV elastomer with excellent performance was prepared. The successful preparation of phosphorus-containing crosslinkers (BPTES) was demonstrated by FT-IR. After the introduction of the new crosslinker, RTV not only has improved flame retardant performance, but also improved mechanical properties. The tensile strength and elongation at break of RTV with 20 wt.% BPTES are increased by 151% and 211%, respectively. The peak heat release rate (pHRR) and the peak of smoke production rate (pSPR) are reduced by 55.9% and 48.6%, respectively, and the thermal stability is also improved. In addition, the successful preparation of HNTs@ZIF was confirmed by FT-IR, XRD, XPS, and TEM. By introducing 2 wt.% HNTs@ZIF into 20 wt.% BPTES cured RTV, the intrinsically flame-retardant RTVs with enhanced performance were prepared. It is worth noting that when 2 wt.% HNTs@ZIF is added, the flame retardant and smoke suppression properties of phosphorus-containing silicone rubber are further improved. Because the ZIF contains cobalt metal ions that can be catalyzed into carbon. The pHRR and pSPR decrease by 18.3% and 16.3%, respectively, and the total heat release (THR) and total smoke production (TSP) decrease by 23.6% and 24.4%, respectively. This work will provide enlightenment for the study of intrinsic flame-retardant RTVs enhanced by modified halloysite.