The invention discloses modified boron-phenolic resin and a preparation method and application thereof. The modified boron-phenolic resin is prepared from, by weight, 65-70 parts of boron-phenolic resin and 50-200 parts of silicate ester and 0.5-2 parts of titanate. The preparation method comprises the steps that silicate ester or titanate are dropwise added into the boron-phenolic resin, and the mixture is mixed to be uniform and reacted at the room temperature for 2-5 h. The modified boron-phenolic resin is still transparent and uniform after being placed at the room temperature for 3 months, no solid matter such as boric acid is separated out, the quality retention rate is also remarkably improved, and the modified boron-phenolic resin can improved product heat stability and fire resistance when used in fire resistance composite materials, functional coatings, an epoxy resin curing agent, a rubber modifying agent and the like. The preparation method is simple, no catalyst is adopted, and the problem that hidden dangers are caused when a catalyst is not thoroughly removed is avoided.