The present invention provides a method and system for synchronously storing multi-modal information of portable endoscope. The method includes: S1: when a mobile terminal acquires data collected by a portable endoscope and updates local data with the acquired data, acquiring update record of the local data of the mobile terminal; and, S2: when the mobile terminal is synchronized with a cloud, synchronizing data in the mobile terminal with data in the cloud by using the update record as information to be synchronized. By creating a table to be synchronized to store change information and location information of files and selectively performing synchronization from the mobile terminal to the cloud or from the cloud to the mobile terminal according to whether or not the table to be synchronized is null during synchronization, unnecessary synchronization operations, storage burden of the mobile terminal and synchronization time and traffic are all reduced.