The invention relates to a method for performing natural soil greening on low-lying saline soil by using a soil conditioner containing chitosan. According to the formula of the soil conditioner, the soil conditioner comprises, by weight parts, 32-34 parts of fermented deer manure, 8-10 parts of sorghum straw powder, 5-7 parts of bentonite, 6-8 parts of biogas residue, 3-5 parts of phosphorite powder, 2-4 parts of chitosan, 2-4 parts of fish bone meal, 1-3 parts of peanut cake, 1-3 parts of egg-shell meal, 2-4 parts of soybean meal, 1-3 parts of ammonium bicarbonate, 1-3 parts of ammonium phosphate, 1-3 parts of ammonium chloride ferric sulfate, 1-3 parts of magnesium hydrogen phosphate, 0.5-0.7 part of phenylacetic acid, 1-3 parts of amino acid salt, 0.2-0.4 part of sodium nitrophenolate, 0.2-0.4 part of brassin, 0.2-0.4 part of gibberellin, 0.1-0.3 part of methanohalophilus zhilinae, 0.1-0.3 part of bacillus coagulans, 0.1-0.3 part of saccharomyces cerevisiae, 0.1-0.3 part of azotobacter vinelandii and 0.1-0.3 part of aspergillus oryzae.