In this paper we describe ground station system architecture for the ground operation of multi pico-satellites. In recent years, many researchers are proposing formation flying mission and constellation mission by using multi-small/pico satellites, therefore ground station system must have the function to operate multi-satellites. We propose the mutli-layered function distributed ground station system, develop it, and operate our pico-satellite CUTE-I and Cute-1.7+APD actually for more 3 years. We describe the details of architecture and the result of the operation of the two pico-satellites.