We calculated the phase diagram of the Kondo-Heisenberg model on two-dimensional honeycomb lattice with both nearest-neighbor and next-nearest-neighbor antiferromagnetic spin exchanges, to investigate the interplay between RKKY and Kondo interactions at presence of magnetic frustration. Within a mean-field decoupling technology in slave-fermion representation, we derived the zero-temperature phase diagram as a function of Kondo coupling J k and frustration strength Q. The geometrical frustration can destroy the magnetic order, driving the original antiferromagnetic (AF) phase to non-magnetic valence bond state (VBS). In addition, we found two distinct VBS. As J k is increased, a phase transition from AF to Kondo paramagnetic (KP) phase occurs, without the intermediate phase coexisting AF order with Kondo screening found in square lattice systems. In the KP phase, the enhancement of frustration weakens the Kondo screening effect, resulting in a phase transition from KP to VBS. We also found a process to recover the AF order from VBS by increasing J k in a wide range of frustration strength. Our work may provide deeper understanding for the phase transitions in heavy-fermion materials, particularly for those exhibiting triangular frustration.