In this paper we investigated numerically the flow and mixing characteristics of the barrier-embedded partitioned pipe mixer (BPPM) in non-creeping flow conditions. Numerical simulations are conducted for three mixing protocols of the BPPM, co-rotational, mirrored co-rotational, and counter-rotational protocols in the range of the Reynolds number (Re), 0.1≤Re≤300, focusing on the effect of the Reynolds number, the barrier height, and the mixing protocols on the mixing in the BPPM. Each mixing protocol creates two crosssectional flow portraits with crossing streamlines. Poincare sections were plotted to investigate the flow system affected by the Reynolds number and the barrier height. Mixing in a specific BPPM is characterized using the intensity of segregation in terms of the compactness and the energy consumption. The dependency of the barrier height and the Reynolds number on the final mixing state of the BPPMs was identified by mixing analyses. The co-rotational protocol results in an efficient mixing in the creeping flow regime. Meanwhile, mirrored co-rotational and counter-rotational protocols, which lead to poor mixing in the creeping flow regime, turned out to be efficient protocols in the higher Reynolds number regime.