We give a theoretical framework to obtain a low-energy effective theory of quantum chromodynamics (QCD) towards a first-principle derivation of confinement/deconfinement and chiral-symmetry breaking/restoration crossover transitions. In fact, we demonstrate that an effective theory obtained using simple but non-trivial approximations within this framework enables us to treat both transitions simultaneously on equal footing. A resulting effective theory is regarded as a modified and improved version of nonlocal Polyakov-loop extended Nambu-Jona-Lasinio (nonlocal PNJL) models proposed recently by Hell, R\"ossner, Cristoforetti and Weise, and Sasaki, Friman and Redlich, extending the original (local) PNJL model by Fukushima and others. A novel feature is that the nonlocal NJL coupling depends explicitly on the temperature and Polyakov loop, which affects the entanglement between confinement and chiral symmetry breaking, together with the cross term introduced through the covariant derivative in the quark sector considered in the conventional PNJL model. The chiral symmetry breaking/restoration transition is controlled by the nonlocal NJL interaction, while the confinement/deconfinement transition in the pure gluon sector is specified by the nonperturbative effective potential for the Polyakov loop obtained recently by Braun, Gies, Marhauser and Pawlowski. The basic ingredients are a reformulation of QCD based on new variables and the flow equation of the Wetterich type in the Wilsonian renormalization group. This framework can be applied to investigate the QCD phase diagram at finite temperature and density.