Waterproof adhesive layer is an important part of the asphalt pavement system for steel bridge decks. To improve the strength and durability of the paving structure, it is necessary to focus on the high-temperature performance and bonding properties of the waterproof adhesive layer. In this paper, Neodymium iron boron magnetic powder (NP) mixed with SBS modified asphalt was used to prepare NP-SBS composite modified asphalt (NSA) for the waterproof adhesive layer material of the steel bridge deck pavement structure. The excellent mechanical and magnetic properties of NP are used to enhance the related properties of the waterproof adhesive layer. The dynamic shear rheometer (DSR) test, the bending beam rheometer (BBR) test, the direct-tensile-loading test, and the direct-shear-loading test with 6 NP contents (0%, 2%, 4%, 6%, 8%, 10%) were conducted to evaluate the high-temperature performance, the low-temperature performance, the tensile strength and the shear strength of the unmagnetized and magnetized NSA. Through these tests, the variation of rheological properties and bonding properties of NSA could be analyzed. The research results showed that the addition of NP improved the high-temperature performance of NSA, but the effect of the powder mortar had an adverse effect on the low-temperature performance. The tensile strength and shear strength of the NSA increased with the increase of the amount of NP, and the amount of 1.0 L/m2 and the NP content of 6% can achieve better bonding properties. After magnetization, the high-temperature performance and bonding properties of NSA will be further improved, but the low-temperature performance will also be further decreased. It reflects the effect of NP on powder modification, magnetic bonding, and magnetic hardening of NSA. The research results show that NSA has excellent high-temperature performance and bonding properties, which can provide a reference for the subsequent research and application of NSA.