The invention provides an intelligent prescription auditing system and an intelligent prescription auditing method. The system is provided with an input module, various databases, a prescription auditing module, a dispensing explaining module, and an output module. The method is implemented as follows: a doctor refines a prescription through the input module and then sends the prescription to the prescription auditing module; after receiving the prescription, the pharmacist reviews writing rules, indications, dosage, incompatibility and drug interactions of the prescription according to various databases; the doctor returns checking comments of the disqualified prescription to the prescription input module so as to modify or re-issue the prescription or give suggestions, and sends the qualified prescription to the dispensing explaining module; after receiving the prescription, an allocation doctor allocates medicines; after receiving the prescription, a dispensing doctor generates prescription information, a medication explaining matter and the like of dispensing explaining, which are printed by the output module and then explained to a patient. The invention provides a medicine dispensing control system and a medicine dispensing control method which are capable of effectively avoiding great prescription, irregular prescription, unsuitable medication for the prescription and unconventional prescription.