To evaluate the effect of full-thickness wedge resection (FTWR) on ocular surface and in vivo confocal microscopy (IVCM) findings in patients with floppy eyelid syndrome (FES). The study included two groups: a surgical treatment (ST) group (26 eyes) consisting of patients who underwent FTWR surgery, and a conservative treatment (CT) group (30 eyes). Pre-treatment and post-treatment ocular surface disease index (OSDI), tear break-up time (TBUT), corneal fluorescein staining (CFS), IVCM findings along with the body mass index (BMI), FES grade, the presence and the treatment of obstructive sleep apnea syndrome (OSAS) were recorded and compared between the groups. The groups were comparable in terms of BMI, FES grade, and OSAS data. After six months, TBUT in the ST group significantly increased to 12.92 ± 1.15, compared to 8.10 ± 1.60 in the CT group (p = 0.000). The CFS and OSDI scores were significantly lower in the ST group (0.15 ± 0.37, 18.0 ± 8.3, respectively) compared to the CT group (0.90 ± 0.61, 27.3 ± 9.3, respectively) (p = 0.000). IVCM analysis revealed a significant decrease in dendritic cell count (ST: 22.0 ± 12.4, CT: 39.5 ± 15.1, p = 0.000) and nerve tortuosity (ST: 1.38 ± 0.64, CT: 2.00 ± 0.59, p = 0.000), with a significant increase in total nerve density (ST: 4.27 ± 0.83, CT: 3.57 ± 0.90, p = 0.002) in the ST group compared to the CT group after six months. In our retrospective cohort, FTWR surgery was shown to be an effective and reliable surgical treatment for FES, improving both ocular surface and IVCM findings. Patients with moderate to severe stages of FES not responding to conservative treatment may benefit from eyelid tightening.