In order to improve the throughput performance and/or economy of a measurement apparatus, the present disclosure provides a metrology apparatus including: a first measuring apparatus; a second measuring apparatus; a first substrate stage configured to hold a first substrate and/or a second substrate; a second substrate stage configured to hold the first substrate and/or the second substrate; a first substrate handler configured to handle the first substrate and/or the second substrate; and a second substrate handler configured to handle the first substrate and/or the second substrate, wherein the first substrate is loaded from a first, second or third FOUP, wherein the second substrate is loaded from the first, second or third FOUP, wherein the first measuring apparatus is an alignment measuring apparatus, and wherein the second measuring apparatus is a level sensor, a film thickness measuring apparatus or a spectral reflectance measuring apparatus.