The invention provides an ex-warehouse optimizing engine system and an optimizing method thereof. The ex-warehouse optimizing engine system comprises a delivery order management module and the like, wherein a PDA login module, the delivery order management module, a PDA order picking module, a PDA encasement module, a PDA inspection module are sequentially connected, and the delivery order management module is mainly used for managing entering, examination and verification and merging of delivery orders. The PDA order picking module is used for PDA order picking and obtaining picking lists of goods to be delivered through inquiry, and a PDA is handheld to perform one-by-one scanning on storage position numbers and commodity numbers and automatically counts the numbers. The PDA encasement module is used for encasement through the PDA. The PDA inspection module inspects whether encased goods are consistent to picked goods or not. The ex-warehouse optimizing engine system performs ex-warehouse operation in a warehouse by adopting the PDA, greatly improves the ex-warehouse accuracy and convenience, decreases various data printed in the warehouse, specifies the ex-warehouse operation process and improves the enterprise efficiency.