A method for in-line measurement of the quality of a microarray are disclosed and the method includes the following steps. A solid substrate is provided, and the solid substrate includes a plurality of areas in an array. At least one biomarker is in-situ synthesized on at least one of the plurality of areas by a plurality of synthesis steps. After performing at least one of the plurality of synthesis step, a check step is immediately performed on a semi-product of the at least one biomarker by an atomic force microscope to obtain an in-line measurement result. The quality of the semi-product of the at least one biomarker is determined based on the in-line measurement result.