The properties of 3D printed products are closely related to the raw materials and the processes by which they are made. The processes of melting, depositing, and cooling of polymers affect the orientation, crystallinity, and microstructure of the product. These in turn influence the thermal, mechanical, optical, and other properties of the printed part. Among various 3D printing methods, filament and pellet extrusion-based fused deposition modeling (FDM) 3D printing is the cheapest and mostly adopted. In this chapter, the devices and some biodegradable polymer materials applicable in FDM 3D printing are briefly introduced. In the first part, preparation and the structure-property relationship of polylactic acid/polybutylene succinate blend filaments are discussed. Rheological, thermal properties of the raw materials and the properties of the printed parts were characterized. In the second part, a pellet extrusion 3D printer with a micro-screw was designed for using pellets of polyhydroxyalkanoate composites, which are difficult to produce filaments. The relationship between the screw parameters of the micro-screw extrusion 3D printer, rheological properties of the composites, and the printed product performance has been investigated. Combining theory and practical application will provide guidance for formulating biodegradable polymer materials and designing equipment for FDM 3D printing.