The present invention discloses a capsule endoscope system, an automatic frame rate adjustment method thereof and a computer readable storage medium. The automatic frame rate adjustment method includes: receiving a first acceleration information ac(t) sensed by a first acceleration sensor in a capsule endoscope; receiving a second acceleration information am(t) sensed by a second acceleration sensor in an external device; calculating and comparing the first acceleration information ac(t) and the second acceleration information am(t) to obtain the relative motion amplitude statem(t) between the capsule endoscope and the external device; adjusting the frame rate of the capsule endoscope according to the relative motion amplitude statem(t), where, the larger the relative motion amplitude statem(t), the larger the frame rate F0(t).