The invention discloses a micro-nano satellite cluster relative positioning method based on a position fingerprint. The method comprises the following steps: S1, setting N dynamic proper stars in a micro-nano cluster as AP of cluster relative positioning, and according to cluster need, establishing a dynamic coordinate system; S2, based on real sampling data and a free-space propagation model, establishing a dynamic fingerprint database; S3, periodically broadcasting by the proper stars; S4, receiving a field strength signal by member stars, and downloading the fingerprint database, thus completing position fingerprint identification; and S5, informing the proper stars of a measuring result of relative positioning by each member star through inter-star directional communication, filteringby the proper stars according to relative motion, thereby acquiring continuous cluster relative positioning information. According to the method provided by the invention, in a process of micro-nano satellite close range cluster formation, a simple omnidirectional antenna is erected, through an existing inter-star communication link device, a relative position relation between the clusters can easily acquired, realizing rapid relative positioning between members in the tight cluster, and space environment is pure, and the device is simple and reliable.