Strongly correlated systems with geometric frustrations can host the emergent phases of matter with unconventional properties. Here, we study the spin $S = 1$ Heisenberg model on the honeycomb lattice with the antiferromagnetic first- ($J_1$) and second-neighbor ($J_2$) interactions ($0.0 leq J_2/J_1 leq 0.5$) by means of density matrix renormalization group (DMRG). In the parameter regime $J_2/J_1 lesssim 0.27$, the system sustains a N{e}el antiferromagnetic phase. At the large $J_2$ side $J_2/J_1 gtrsim 0.32$, a stripe antiferromagnetic phase is found. Between the two magnetic ordered phases $0.27 lesssim J_2/J_1 lesssim 0.32$, we find a textit{non-magnetic} intermediate region with a plaquette valence-bond order. Although our calculations are limited within $6$ unit-cell width on cylinder, we present evidence that this plaquette state could be a strong candidate for this non-magnetic region in the thermodynamic limit. We also briefly discuss the nature of the quantum phase transitions in the system. We gain further insight of the non-magnetic phases in the spin-$1$ system by comparing its phase diagram with the spin-$1/2$ system.