Femtosecond laser two-photon three-dimensional optical data storage is an effective method for high capacity data storage. In this paper, system construction is analyzed in detail from hardware and software aspects for dual pick-up head three-dimensional optical storage systems. Three-dimensional optical storage system is conposed of the fluorescence reader module and the servo control module, firstly analyzes the read and write process of three-dimensional optical storage by 89c52 MCU controling from the hardware. Then, the software is analyzed in detail, the software consists of two parts: the lower computer software and PC software. lower computer software achieves communication and control related to hardware, PC software is used to facilitate the control of the experimental system. Two CPU control software is introduced, and controlling process of PC software control is analyzed in detail. These work has laid a solid foundation for the practical of three-dimensional optical storage technology.