Thin-walled structures, as common component specification for aerospace components, easily experience deformation and chatter issues during machining (e.g. milling) operations. With Additively Manufactured (AM) materials being increasingly applied in these areas, it is found that their microstructural anisotropy can lead to varied mechanical properties and machinability in different directions. However, former research on thin-walled parts mainly focused on bulk materials, while the machining performance of these thin-wall structures produced from AM processes remains unclear. In this view, this research aims to reveal the effect of microstructural anisotropy resulting from AM process on the machining (deformation and stability) of thin-walled parts by taking Ti6Al4V as an example. Three kinds of AM Ti6Al4V thin-walled parts were fabricated with different laser scanning strategies, in which the prior columnar β grains were found to grow along the building direction and led to a variation in mechanical properties. Owing to this, the deformation and machining stability varied in the AM thin-walled parts with different β phase crystallization orientations on the same milling directions, which could be attributed to the changes of cutting force and dynamic parameters (e.g., frequency, stiffness (determined by elastic modulus), damping ratio) in different orientations. This investigation could provide a reference for the selection of printing strategies and follow-up machining process of AM thin-walled parts when considering their microstructural anisotropy.