Tissue engineering is expected to construct complicated hominine organs composed of many different types of cells. One of the key points is the accurate controlling of scaffold material and porous morphology point by point. A new direct rapid prototyping process called low-temperature deposition manufacturing (LDM) was proposed to fabricate scaffolds. The new process integrated extrusion/jetting and phase separation and therefore could fabricate scaffolds with hierarchical porous structures creating a wonderful environment for the growth of new tissue. The interconnected computer-designed macropores allow cells in the new tissue to grow throughout the scaffold. Also, the parameter-controlled micropores let nutrition in and metabolic wastes out. The macrocellular morphology, microcellular morphology, porosity, and mechanical properties of the poly(alpha-hydroxy acid)-TCP composite scaffolds prepared by the proposed method are investigated. These scaffolds with high controllability would potentially play an important role in tissue engineering. LDM could also be combined with multinozzle deposition or cell deposition to exactly control materials or cells point by point. This might bring a breakthrough to the engineered fabrication of complicated organs.