Background Nipple reconstruction using local skin flap leaves no morbidity in the healthy nipple. However, one disadvantage of this procedure is that the projection is not often maintained. There are few reports on the rate of long-term maintenance of nipple projection. This study aimed to analyze the 5-year results of clover flap (C-F) nipple reconstruction to determine whether it can be used to maintain nipple projection for long periods and to investigate the factors involved in maintenance of nipple projection. Methods Patients that underwent nipple-areola reconstruction using C-F after undergoing a two-stage implant-based breast reconstruction with skin-sparing mastectomy between January 2012 and December 2019 were included. The projection of the reconstructed nipple was measured annually for 5 years postoperatively, and the nipple projection maintenance rate (%) was calculated. The influence of eight factors, namely smoking, irradiation, scarred skin, flap pedicle relative to the mastectomy scar, location of the mastectomy scar, flap suturing, and flap necrosis, on nipple height were evaluated. Results Overall, 275 patients were enrolled. The average maintenance rates (%) at 1-5 years after surgery were 47.1, 39.8, 36.4, 34.6, and 33.5. Creating a well-vascularized skin flap, designing the pedicle farther away from the mastectomy scar, choosing a surgical technique involving an oblique scar on the side of the nipple by wrapping the skin flaps, and including an appropriate amount of fat tissue inside the reconstructed nipple are important for nipple projection maintenance. Conclusion Nipples reconstructed using the C-F technique on the artificial mound achieve excellent long-term result.