A substrate inspection method includes a first process of taking, while rotating a holding table where a reference substrate is held, an image of an end surface of the reference substrate; a second process of obtaining shape data on the end surface of the reference substrate by processing the image; a third process of taking, while rotating the holding table where a target substrate is held, an image of an end surface of the target substrate; a fourth process of obtaining shape data on the end surface of the target substrate by processing the image; and a fifth process of calculating a warpage amount of the target substrate by obtaining a difference between the shape data obtained in the second process and in the fourth process under a condition that a rotational position of the holding table in the first process coincides with that in the third process.