A fully automatic microscopic scanner, comprising an image acquisition mechanism (IAM) with a line array camera. The IAM and the microscopic scanning mechanism move along X/Y/Z axis under the action of a power control mechanism. The light source mechanism illuminates an area greater than or equal to the total area of the tray and has a flat light source with a condenser, a cooling fan, a water cooling unit. A general control mechanism and a laser pre-focus system connects to the light source mechanism. The fully automatic microscopic scanner links the microscopic scanning mechanism and the IAM with the light source mechanism. Flexible adjustment of lens is achieved by making the lens move forwards and backwards, leftwards and rightwards and up and down. The light source mechanism and laser pre-focus system, the stage and the light source are fixed during the scanning process to achieve real-time accurate and fast focusing.