Process kinetics can present necessary information for granular anammox process but little study focused on the nitrogen removal kinetics of pilot-scale anammox granular process is available. In this study, the substrate removal kinetics in a pilot-scale anammox granular reactor were investigated by inoculating anammox granules in to an UASB reactor, which was then operated at different hydraulic retention times and nitrogen loading rates. The reactor showed good tolerance to substrate concentration shock while it was affected significantly by hydraulic shock. Molecular techniques confirmed the existence of at least four well-known anammox species and anammox cells accounted for 93.7% of total cells. Evaluation of the nitrogen removal kinetics indicated that the Grau second-order substrate removal model and the modified Stover–Kincannon model turned out to be appropriate to describe nitrogen removal of anammox granules, rather than the first-order substrate removal model, the Monod model, and the Contois model. Model evaluation was then carried out via assessing the linearity between the experimental data and predicted values, which proved the applicability of the two models. The information derived from the current study could guide and optimize the design of full-scale anammox granular reactors.