The invention relates to a software version updating method and system. The software version updating method comprises the steps that a new version is uploaded to a main server; the main server sends the new version to a sub-server with the version permission; a client-side requests to update the version when detecting the new version; when the client-side has the right to obtain the new version, the main server sends the download link of the new version to the client-side; the client-side has access to the download link, downloads the configuration information of the version, and then judges whether the configuration information of the version and the configuration information of an old version are completely the same or not, if the configuration information of the version and the configuration information of the old version are completely the same, the configuration information of the version is deleted, and the process is ended, and if the configuration information of the version and the configuration information of the old version are not completely the same, it is determined to update a file list, and an appointed file is downloaded from the sub-server; the client-side closes the old version and carries out backup, the downloaded file replaces the old file, whether software is normally started or not is judged, the updating of the software succeeds if the software is normally started, and the updating of the software fails if the software is not normally started. The software version updating method and system can reduce loads of the server, increase the updating speed of the software version and ensure that the client-side can be provided with the correct new version all the time.