The invention discloses a positioning method, a positioning device and a storage medium of a spacecraft. The positioning method comprises the following steps of A, measuring estimation distances between the spacecraft and at least two base stations; B, according to the estimation distances, calculating standardizing factors, wherein the standardizing factors are used for measuring the difference between the estimation distance and the real distance between the spacecraft and the base station; C, according to the standardizing factors and the flight height of the spacecraft, converting the estimation distances into the standard distance between the spacecraft and the base station in a reference plane; D, according to the standard distance, applying an OTDOA (observed time difference of arrival) positioning algorithm to calculate the positioning information of the spacecraft. The whole positioning calculation method has the advantages that the positioning accuracy in horizontal height and vertical height can be well improved, and the complexity in calculation is low; compared with the existing positioning algorithm, the compatibility is better.