The invention provides an intensive storage refrigeration warehouse system. The intensive storage refrigeration warehouse system comprises a manual operation area subsystem, a refrigeration area subsystem and a telescopic conveying line. A goods sorting and information inputting device of the manual operation area subsystem sorts goods and inputs goods information into a management information system of the intensive storage refrigeration warehouse system, and then the goods are conveyed by a first warehousing conveying line. The refrigeration area subsystem comprises a second warehousing conveying line, a plurality of kinds of SKU intensive storage channels and a multi-layer shuttling lifting trolley, when the goods input operation is executed by the intensive storage refrigeration warehouse system, the second warehousing conveying line receives the goods conveyed by the first warehousing conveying line, and then the multi-layer shuttling lifting trolley puts the goods to the preset various SKU intensive storage channels according to an instruction of the management information system; the telescopic conveying line is arranged between the manual operation area subsystem and the refrigeration area subsystem. The warehousing, sorting and ex-warehouse efficiency of a refrigeration warehouse can be improved, cost is reduced, and the defect of manually working in a low-temperature environment is avoided.