Organic micro- or nanocapsules are widely used as reservoirs to carry sealing agents or corrosion inhibitors to achieve the self-healing functionality of coatings. To understand the impact of the capsules' incorporation on the barrier properties of organic coatings, composite epoxy resin coatings containing different concentrations (e.g., 5 wt%, 10 wt% and 20 wt%) of urea-formaldehyde (PUF) microcapsules were deposited on the top of Q235 carbon steel. The features of PUF microcapsules and composite coatings were characterized, and the corrosion behaviors of the coating-protected carbon steel were investigated in NaCl solution. The results showed that the spherical PUF microcapsules (∼40 μm) with 290 nm thick shell and hexyl acetate core are synthesized through in situ polymerization. The prepared microcapsules can uniformly distribute within the epoxy resin coatings, which in turn deteriorates the corrosion resistance of the microcapsules-containing composite coatings (MCECs). Lower volume (5 wt%) microcapsules incorporation caused a slight reduction in the corrosion resistance (Rc) and effective capacitance (Ceff) from 4.39 × 107 Ω·cm−2 and 6.50 × 10−5 mF·cm−2 to 8.72 × 106 Ω·cm−2 and 5.63 × 10−5 mF·cm−2, respectively. For higher volume (10 wt% and 20 wt%) groups, the Rc further decreases to 7.47 × 105 Ω·cm−2 and 1.45 × 105 Ω·cm−2, whereas the Ceff increases to 5.63 × 10−5 mF·cm−2 and 5.63 × 10−5 mF·cm−2, respectively. The failure mechanism of the MCECs can be ascribed to the rupture of the PUF microcapsules during the curing process and/or immersion in NaCl electrolyte, which suggested the mechanical strength and chemical stability of the capsules should be carefully determined to avoid their negative impact on the barrier property of polymeric coatings.