To investigate the histomorphometric performance of two-stage maxillary sinus floor elevation (TMSFE) with various bone substitutes in the treatment of atrophic posterior maxilla. Four databases (PubMed, Embase, Web of Science, and The Cochrane Library) were searched from the beginning of database establishment to August 8, 2023. The included articles were limited to the English language. A systematic search was performed to identify randomized controlled trials assessing the histological performance of various biomaterials in TMSFE with a follow-up of 5-8 months. The main outcome was an area of new bone, and an additional outcome was residual graft material. Extracted data were analyzed by using a Bayesian approach (the Markov chain Monte Carlo) to establish ranks of various biomaterials in R language. Finally, the search identified 22 studies that reported 22 trials on bone area (17 kinds of biomaterials) and 12 studies on residual graft materials (12 kinds of biomaterials) after the exclusion of one study disconnected from the network plot. No local inconsistency could be found in studies regarding bone formation, while no closed loop was detected in residual graft material. The top 3 probabilities of biomaterials in terms of bone formation were Allograft + Xenograft (AG + X) (87.14%), X + Polymer (75.69%), and Autogenous Bone + Bioactive Glass (AB + BG) (71.44%). AG + X had the highest probability (87.14%) of being the most optimal treatment for bone formation. Biphasic calcium phosphate + Fibrin sealant (BCP + FS) was ranked as the slowest absorbing biomaterial (78.27%) in TMSFE. Within the limitations of the current network meta-analysis, AG + X may represent an optimal biomaterial for bone formation in TMSFE. The use of X in combination with other biomaterials demonstrates superior osteogenic effects in TMSFE. BCP + FS exhibited strong mechanical properties during a short-term observational period. The present findings suggest that AB is not the only feasible standard for bone grafts.