The application of mainstream anammox process is hampered by its overlong start-up and instability under disturbance. A lab-scale mainstream anammox moving bed biofilm reactor (MBBR) was successfully started in 120 days with stepwise decrement in influent nitrogen concentration from sidestream to mainstream condition. The initial colonization by Candidatus Jettenia and filamentous fermenter Anaerolineaceae were potentially mediated by hydrophobic interaction and type IV pilus. Ca. Kuenenia with higher substrate affinity outcompeted Ca. Jettenia, and the predominant fermenters shifted to fermentative Ignavibacteriaceae in the mature biofilm. A novel mainstream anammox biofilm development (MABD) model was constructed to describe biofilm growth, population dynamics, and nitrogen removal performance. The simulation results suggested that higher inocula biomass (460–690 mgVSS·L−1), relative abundance of low-affinity AnAOB in the inocula (e.g., Ca. Jettenia, 1.3–2%), and the early-stage solids retention time (45–68 days) were desired to form thicker biofilm and improve effluent quality during 120-day mainstream anammox MBBR start-up. The mechanistic insights into biofilm formation and predictive power of the newly developed MABD model are of importance to the design and operation of mainstream anammox processes towards more biofilm biomass and higher nitrogen removal efficiency.