Scaffolds with intrinsically interconnected porous structures are highly desirable in tissue engineering and regenerative medicine. In this study, three-dimensional polymer scaffolds with highly interconnected porous structures were fabricated by thermally induced phase separation of novel synthesized biodegradable poly(propylene fumarate)-co-poly(l-lactic acid) in a dioxane/water binary system. Defined porous scaffolds were achieved by optimizing conditions to attain interconnected porous structures. The effect of phase separation parameters on scaffold morphology were investigated, including polymer concentration (1, 3, 5, 7, and 9%), quench time (1, 4, and 8 min), dioxane/water ratio (83/17, 85/15, and 87/13 wt/wt), and freeze temperature (−20, −80, and −196 °C). Interesting pore morphologies were created by adjusting these processing parameters, e.g., flower-shaped (5%; 85/15; 1 min; −80 °C), spherulite-like (5%; 85/15; 8 min; −80 °C), and bead-like (5%; 87/13; 1 min; −80 °C) morphology. Modulation of phase separation conditions also resulted in remarkable differences in scaffold porosities (81% to 91%) and thermal properties. Furthermore, scaffolds with varied mechanic strengths, degradation rates, and protein adsorption capabilities could be fabricated using the phase separation method. In summary, this work provides an effective route to generate multi-dimensional porous scaffolds that can be applied to a variety of hydrophobic polymers and copolymers. The generated scaffolds could potentially be useful for various tissue engineering applications including bone tissue engineering.