Addition of microcapsules with a high dielectric constant and low specific heat capacity to a battered layer was designed to create a higher temperature in the crust than in the prefried fish nuggets to prevent the water vapor in the fish nuggets from migrating to the crust during microwave heating. Therefore, chitosan-silica hybrids and soybean oil were utilized to prepare the shell and core of the thermally stable microcapsules (MC(CS)), respectively. The MC(CS) were prepared by sol-gel coacervation from an oil-in-water emulsion. The sodium silicate was hydrolyzed and coacervated through polymerization for 24 h at pH 5. The zeta potential analysis indicated that chitosan with a positive charge and silica with a negative charge interacted through electrostatic attraction to form a hybrid shell. The volume mean particle size and encapsulation efficiency of the MC(CS) were 9.6 ± 0.2 μm and 75.6% ± 1.3%, respectively, when oil/chitosan = 0.2 and chitosan/silica = 0.5 (w/w). In addition to H-bonding and electrostatic attraction, Si-O-N bonds were formed between chitosan and silica. Dehydration of the bound water in the MC(CS) was observed in the range of 25 to 250 °C in the differential scanning calorimetry thermal analysis, with the lack of apparent thermal peaks indicating its high thermal stability. The decrease of force to cut the crust observed by texture analysis as well as the increase of hedonic score by consumer acceptance test revealed the addition of 1% MC(CS) significantly improved the crispness of the crust in the microwave-reheated nuggets.