Quercetin (Que) is an important bioactive compound; however, its application in food systems is limited by its low aqueous solubility, poor stability, and limited bioaccessibility. To improve the stability and utilization efficiency of Que, delivery systems based on poly(tannic acid) (PTA) and the metal-phenolic networks PTA-Cu and PTA-Fe were constructed. Their encapsulation performance, structural characteristics, thermal stability, in vitro simulated gastrointestinal digestion behavior, apparent equilibrium solubility, and antioxidant activity were systematically evaluated. The results showed that the encapsulation efficiencies of Que in PTA@Que, PTA-Cu@Que, and PTA-Fe@Que were 89.52%, 99.76%, and 99.41%, respectively. Metal coordination increased the particle size of the Que-loaded systems from 0.69 μm to 1.02-1.40 μm while decreasing the polydispersity index (PDI) from 0.31 to 0.15-0.17, accompanied by changes in the local chemical environment of functional groups and molecular packing. After treatment at 70 °C for 8 h, the Que retention rates of PTA@Que, PTA-Cu@Que, and PTA-Fe@Que were 59.26%, 67.53%, and 64.39%, respectively, all of which were higher than that of free Que (39.53%). At the end of simulated gastrointestinal digestion, the proportion of Que in the micellar fraction of PTA-Cu@Que reached 63.19%, which was 3.29-fold that of free Que. The apparent equilibrium solubilities of Que in PTA-Cu@Que at 37 and 70 °C were 9.00 and 16.67 mg·mL-1, respectively, compared with 4.53 and 6.42 mg·mL-1 for free Que. At a concentration of 30 μg·mL-1, the ABTS·+ and DPPH· radical scavenging activities of PTA-Cu@Que reached 97.82% and 89.29%, respectively. These results demonstrated that metal–phenolic networks enhanced the encapsulation efficiency of Que, improved its thermal stability, apparent solubility, and in vitro bioaccessibility, and maintained favorable free-radical scavenging activity. Among the tested delivery systems, PTA-Cu@Que exhibited comparatively superior overall performance. This study provides a theoretical and practical basis for the development of novel delivery platforms for the stabilization and efficient utilization of Que in food systems.