It is of great importance to protect paper cultural relics, especially in terms of making them waterproof. One of the important ways to protect paper cultural relics is by hydrophobic modification treatment. However, most of the existing hydrophobic modification methods rely on a great deal of organic solvents, which poses greater risks to safety and pollution. In this work, a simple, green, and effective method for paper hydrophobic treatment was proposed and evaluated. The vapor of a fluorinated triethoxysilane was reacted with the active hydroxyl group on the paper in a closed space, which realized the hydrophobic modification of the paper in one step. The contact angle of the hydrophobic paper prepared by this method was 148.4° under optimal experimental conditions. In addition, this method did not damage the paper, based on the results of the scanning electron microscopy of the paper before and after hydrophobic treatment. The generality of this method was verified by using other substrates and hydrophobic reagents. This method is simple to operate and does not require the usage of a large amount of organic reagent. It is expected to receive widespread attention in the field of the protection of paper and wooden cultural relics.