In the SSA22 field which exhibits a large-scale proto-cluster at z=3.1, we carried out a spectroscopic survey for Lyman Break Galaxies (LBGs) with the VLT/VIMOS and identified 78 confident LBGs at z=2.5-4. We stacked their spectra in the observer's frame by using a sophisticated method. Analysing the composite spectrum, we have revealed that the large-scale proto-cluster at z=3.1 has a strong HI absorption dip of rest-frame equivalent width of -1.7{AA}. Another strong absorption dip found at z=3.28 is associated with a modestly high-density LBG peak, similar to that at z=3.1. We have also detected an HI transparency peak at z=2.98 in the composite spectrum, coincident with a void in the LBG distribution. In this paper, we also investigated the relation between LBGs, HI gas, and active galactic nuclei (AGNs) at z=3-4 in the SSA22 field. Two AGNs at z=3.353 and 3.801 are, respectively, associated with the LBG concentration of an overdensity factor {delta}_LBG_~2 in the present statistics. Another structure at z=3.453 is remarkable: 20 comoving Mpc-scale dense HI gas which is not associated with any apparent LBG overdensity but involving a pair of AGNs. Such structure may be a new type of the AGN-matter correlation. If the inhomogeneous structures over a comoving Gpc scale found in this paper are confirmed with sufficient statistics in the future, the SSA22 field will become a key region to test the standard cold dark matter structure formation scenario.