The invention relates to a method for protecting data in mobile storage equipment, which is used for preventing the data in the mobile storage equipment from being randomly transmitted in different network environments such as intranet or extranet. The mobile storage equipment is divided into three physical partitions, namely an intranet zone, an auditing zone and an extranet zone, and application software with resource management, user login setting and network environment detection functions is embedded into the mobile storage equipment; the mobile storage equipment can exchange the data with a computer only through a self-contained resource manager, and prohibits a resource manager of a computer operating system from accessing a storage file in the mobile storage equipment; and only the content of the extranet zone is displayed when the mobile storage equipment is in the extranet network environment and the contents of the intranet zone, the extranet zone and the auditing zone are displayed when the mobile storage equipment is in the intranet network environment through the embedded software, and only an administrator can copy data from the intranet zone and the auditing zone of the intranet computer or the mobile storage equipment to the extranet zone of the mobile storage equipment through special auditing software, so that the information safety of the intranet is protected.