Isovalent substitution of Zr4+ for smaller Ti4+ was performed in the 8-layer twinned hexagonal perovskite (referred to as 8H) tantalate Ba8Ti3Ta4O24, which stabilizes a 10-layer twinned hexagonal perovskite (referred to as 10H). The formation of the 10H phase occurs at low substitution concentration (x = 0.1) in Ba8ZrxTi3-xTa4O24 at 1300 degrees C and reverts back to the 8H phase upon heating at elevated temperatures. Such a 10H-to-8H phase transformation is suppressed at higher Zr-substitution contents (x > 0.1). The approach combining simulated annealing and Rietveld refinement with compositional constrain indicates that the 10H Ba8Zr0.4Ti2.6Ta4O24 (x = 0.4) composition adopts a simply P6(3)/mmc disordered structure with Zr cations preferably located in corner-sharing octahedral (CSO) sites compared to face-sharing octahedral (FSO) sites. This 8H-10H phase competition, dependent on the substitution of Zr4+ for Ti4+ and firing temperature, is discussed in terms of the FSO B-B repulsion controlled by the cationic size, as well as the stacking periodicity which affects the thermodynamic stability. Both 8H- and 10H-phase pellets of Ba8ZrxTi3-xTa4O24 exhibit comparable and poorer microwave dielectric properties than the parent 8H Ba8Ti3Ta4O24, which is characterized by cationic disorder and FSO B-B repulsion. The 8H and 10H Ba8ZrxTi3-xTa4O24 ceramics display electrical insulator behavior but with electrically heterogeneous microstructure on the bulk grains. This study demonstrates the opportunity to control the stacking periodicity for the twinned hexagonal perovskites via tuning the B-cationic size and the firing temperature.