We have performed hard x-ray photoemission spectroscopy (HAXPES) for Yb-based Kondo lattice compounds; an antiferromagnetic heavy-fermion system YbNi3Al9 and a valence fluctuation system YbNi3Ga9. The Yb 3d5/2 spectra of YbNi3Ga9 showed both Yb2+ and Yb3+-derived structures indicating strong valence fluctuation, and the intensity of Yb2+ (Yb3+) structures gradually increased (decreased) on cooling. The Yb 3d5/2 spectra of YbNi3Al9 mostly consisted of Yb3+-derived structures and showed little temperature dependence. The Yb valences of YbNi3Ga9 and YbNi3Al9 at 22 K were evaluated to be 2.43 and 2.97, respectively. Based on the results of the Ni 2p and valence-band HAXPES spectra together with soft x-ray valence-band spectra, we described that the difference of physical properties of YbNi3X9 (X= Al, Ga) is derived from the differences of the 4f-hole level relative to the Fermi level (EF) and Ni 3d density of states at EF. The HAXPES results on the Yb valences were consistent with those obtained by x-ray absorption spectroscopy using the partial fluorescence yield mode and resonant x-ray emission spectroscopy at the Yb L3 edge.