As large span steel bridges develop rapidly, the type of steel deck paving is also diversifying. However, the current steel deck paving layer is a dense-graded mixture of both upper and lower layers. This makes it difficult for water to drain out of the dense deck when it enters the interior of the deck, and the deck is easily damaged by the traffic load. This paper aims to prolong the service life of the pavement and solve the problem that the pavement is prone to water damage under the existing pavement system. In this paper, a new steel bridge deck paving system is formed by developing a new type of waterproofing binder layer material and developing an open-graded paving layer underlayment. Through indoor tests and finite element software analysis, the effect of the environment on the pull-out strength of the waterproofing binder layer material under different permaculture conditions is investigated; a suitable void ratio control range for the paving layer is explored through paving layer seepage analysis and indoor tests. The study revealed that the new epoxy resin waterproofing bonding layer was able to maintain a large pull-out strength value in a 60 °C water bath for 2 weeks. The paving with void ratios of 18, 20, and 22% were all able to drain 50% of the water inside the paving within 2 h, with excellent drainage capacity. Based on the modeling analysis and indoor test results, the target void ratio of the asphalt mix under the pavement is recommended to be controlled at 20–22%, with a void ratio in this range to solve the problem of water entering the steel bridge deck pavement and causing pavement distress.