Here, spontaneous lamellar alignment in a thickness-modulated block copolymer film is presented as a facile, scalable, and general approach for creating a highly aligned lamellar morphology. Thickness-modulated block copolymer films are prepared on neutral surfaces by various methods, such as solution dropping, dewetting-induced self-organized patterning, and thermal imprinting. Regardless of the film preparation method, the self-assembled lamellar domains become spontaneously aligned along the thickness gradient after sufficient thermal annealing. Real-time AFM imaging reveals that spontaneous alignment occurs through the directional growth of well-ordered domains along the thickness gradient, which is accompanied by defect dynamics, with vertical linear defects moving from thicker parts of the film towards the thinner ones, reducing their length and thus the associated energy. The mechanism underlying this interesting self-aligning behavior is provided by a ‘geometric anchoring’ phenomenon, originally envisioned to account for the liquid crystal alignment under a non-flat geometry of confinement. This novel self-aligning principle offers a valuable opportunity to control nanoscale alignment in block copolymer films by manipulating the, much larger, microscale morphology.