Simultaneous incorporation of elastomer and nanofillers into polymers is a facile route to develop high-performance polymer composites with balanced properties. It has been demonstrated that the properties of the composites largely depend on its phase morphologies, however, less attention has been paid on the role of the self-organization between elastomer and fillers in determining the phase morphology. In this work, polyurethane (PU) toughened biodegradable polylactide (PLA) has been selected as the model blend. The first example is the utilization of carbon black (CB) nanoparticles with good self-networking capability in polymer melts to tailor the phase morphology of PLA/PU (85/15) blend. Interestingly, the change of the phase morphology from common droplet structure to unique co-continuous like structure (composed of discontinuous irregular PU domains) is observed with the addition of some amounts of CB due to the self-networking effect of the nanoparticles as well as the strong affinity between PU phase and CB particles. The formation of the co-continuous like morphology can impart the blend with a good stiffness-toughness balance or even an excellent electrical conductivity. Another example is the use of carbon fibers with ultra-high modulus and electrical conductivity as fillers to effectively enhance the blend properties. It is interesting to find that PU phase can serve as “solder” to weld CF into a more perfect network because PU has stronger interaction with CF as compared with PLA. The formation of self-weld network structure constructed by both stiff CF and ductile PU elastomer can simultaneously improve tensile strength, impact toughness and even electrical conductivity of PLA. Our works not only provide two efficient but low-cost strategies to prepare PLA-based composite with a good stiffness-toughness balance but also give a deep insight into the relationship between phase morphology and properties of polymer/elastomer/fillers composites.