Abstract: Marine engineering is associated with complex and harsh corrosive environments. In this regard, organic coatings are the most cost-effective and widely used anti-corrosion method. Nanomaterial-modified weather-resistant polyurethane powder coatings offer excellent properties such as aging resistance, acid and alkali resistance, and salt spray resistance. Moreover, they can be used as an outdoor, super-weather-resistant coating or a marine anti-corrosion system surface coating. Fluorocarbon coating with ethylene fluoride and vinyl ether (FEVE) exhibits excellent chemical corrosion resistance, temperature resistance, and ultralong weather resistance, thus rendering it a suitable anti-corrosion option for high-end marine equipment. This study refers to the cyclic corrosion test method specified in the ISO 20340: 2009 standard and combines it with possible practical application environments such as the South China Sea to remove the low-temperature exposure step at −20 °C, which does not apply in actual operating conditions. Finally, the indoor cyclic accelerated aging test procedure of ultraviolet (UV) aging, condensation, and salt spray tests is determined. Accelerated aging tests are conducted on two marine high-performance anti-corrosion coating systems, namely, a nano-modified phenolic epoxy heavy-duty anti-corrosion powder coating for the primer and a nano-modified polyurethane weather-resistant powder coating and FEVE fluorocarbon super-weather-resistant powder coating for the topcoat, for a total of 38 aging cycles. Samples are retrieved for testing and analysis after 6, 12, 18, 25, 31, and 38 cycles, with one set of blank samples reserved. By testing the glossiness as well as performing SEM (scanning electron microscope), FTIR (Fourier transform infrared), and scribe corrosion analysis on the samples after different aging cycles, changes in the gloss loss rate, surface microstructure, chemical functional group composition, and corrosion width at scribe with aging time are analyzed. The results show that during 38 cycles of the accelerated aging test, the glossiness, microstructure, and chemical functional groups of the two coatings change marginally as aging progresses. The FEVE fluorocarbon super-weather-resistant coating performs slightly better than the nano-modified polyurethane weather-resistant coating in terms of light retention and chemical stability. Between the two coatings, the nano-modified polyurethane weather-resistant coating exhibits coating blistering earlier. The topcoat’s inferior mechanical properties and low compatibility with the primer affect the peeling of the topcoat and primer of the FEVE fluorocarbon coating in the early stage of aging. Based on the corrosion width at the scribe, the long-term aging resistance of the FEVE fluorocarbon super-weather-resistant coating is superior to that of the nano-modified polyurethane weather-resistant coating. The corrosion-protection performance of both coating systems is dominated by the primer at the marked line before 18 aging cycles and by the topcoat after 18 aging cycles. Fluorocarbon resin in fluorocarbon coatings comprises highly efficient C—F covalent bonds and exhibits strong inertness; therefore, it is highly resistant to ultraviolet radiation. As aging progresses, the advantages of the fluorocarbon coating over the polyurethane coating in terms of UV aging resistance become more apparent gradually. Both coatings are powder coatings, environmentally friendly, and pollution-free. FEVE fluorocarbon coatings offer better aging resistance than polyurethane coatings; however, fluorocarbon coatings cost more than polyurethane coatings. Therefore, to satisfy the same weather-resistance requirements, polyurethane coatings are more affordable than FEVE fluorocarbon coatings.