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 . Analyzing the composite spectrum , we have revealed that the large-scale proto-cluster at z = 3.1 has a strong H i absorption dip of rest-frame equivalent width of -1.7 Å . 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 H i 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 , H i gas and 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 } \simeq 2 in the present statistics . Another structure at z = 3.453 is remarkable : 20 comoving Mpc scale dense H i 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 .