This study aims to evaluate the economy of a steel bridge deck pavement scheme (SBDPS) using a comprehensive life-cycle cost (LCC) analysis approach. The SBDPS are divided into the “epoxy asphalt concrete system”(EA system) and“ Gussasphalt concrete system”(GA system) according to the difference in the material in the lower layer of the SBDPS. A targeted LCC checklist, including manager cost and user cost was proposed, and a Markov-based approach was applied to establish a life-cycle performance model with clear probability characteristics for SBDPS. Representative traffic conditions were designed using a uniform design method, and the LCC of SBDPS under representative traffic conditions and different credibility (construction quality as a random factor) was compared. The reliability of the LCC analysis approach was verified based on the uncertainty analysis method. Based on an expert-scoring approach, a user cost weight was obtained to ensure it is considered reasonably in the LCC analysis. Compared with the cumulative traffic volume, the cumulative equivalent single axle loads (CESAL) have a closer relationship with the LCC. The GA system has better LCC when the CESAL is less, while the EA system is just the opposite. The breaking point of CESAL for the LCC of the EA system and the GA system is 15 million times. The LCC analysis of SBDPS should consider the influence of random factors such as construction quality. The comprehensive LCC analysis approach in this paper can provide suggestions for bridge-management departments to make a reasonable selection on SBDPS.