The invention discloses an organic fertilizer containing furfural slag and biological bacteria, as well as a preparation method thereof. The organic fertilizer containing furfural slag and biological bacteria comprises components in parts by weight as follows: 15 parts of furfural slag, 13 parts of chicken manure, 5 parts of amino acid, 15 parts of humic acid, 12 parts of bone powder, 20 parts of xylogen, 15 parts of bentonite and 5 parts of biological bacteria; the furfural slag is waste furfural slag generated in a furfural slag production process; and the biological bacteria are a mixture of one or more than two of bacillus megatherium, rhizobium japonicum, purple perilla rhizobium and an EM (effective microorganism) flora. According to the organic fertilizer containing furfural slag and biological bacteria, as well as the preparation method thereof, a large amount of furfural slag is added in the effective components, so that contents of CO3<2->and HCO3<-> in the soil can be reduced, physical and chemical properties of soil are effectively improved, and alkalinity of soil is reduced; and further, the content of the furfural slag in the organic fertilizer is higher, during application, Cl<-> can be further reduced, contents of elements such as organic matters, potassium, nitrogen and the like in salinity soil are increased, and the elements and other nutritional ingredients in the organic fertilizer are combined to promote growth of crops.