Besides its application in media printing, drop-on-demand (DoD) printing is becoming an attractive alternative to traditional micro-fabrication to build 3D structures with wide applications. In DoD printing, each type of nozzle (ejector) has its uniqueness and limitation in the dispensing material properties, driving parameters, and the ejected droplet dimension. This paper presents a multi-nozzle DoD printing machine to satisfy the increasing demand for multi-material dispensing in industry. On the hardware aspect, a microcontroller-based synchronizer is designed to synchronize the printing process from multi-nozzles with respect to a movable positioning stage. This real-time control contributes to accurate micro-droplet deposition. On the software aspect, a three-layer framework is proposed, including user interface, system manager, and hardware interface layer. This proposed structure greatly improves the system flexibility with which the user can dynamically configure the desired dispensers for 3D structure printing. Integrating these techniques into the printing system, the developed DoD system can achieve a flexible and friendly user interface, while dispensing a wide range of functional materials using various types of dispensing nozzles.