Prolonged mechanical ventilation (PMV) is associated with poor outcomes and a high economic cost. The association between protein intake and PMV has rarely been investigated in previous studies. This study aimed to investigate the impact of protein intake on weaning from mechanical ventilation. Patients with the PMV (mechanical ventilation ≥6 h/day for ≥21 days) at our hospital between December 2020 and April 2022 were included in this study. Demographic data, nutrition records, laboratory data, weaning conditions, and survival data were retrieved from the patient’s electronic medical records. A total of 172 patients were eligible for analysis. The patients were divided into two groups: weaning success (n = 109) and weaning failure (n = 63). Patients with daily protein intake greater than 1.2 g/kg/day had significant shorter median days of ventilator use than those with less daily protein intake (36.5 vs. 114 days, respectively, p < 0.0001). Daily protein intake ≥1.065 g/kg/day (odds ratio: 4.97, p = 0.033), daily protein intake ≥1.2 g/kg/day (odds ratio: 89.07, p = 0.001), improvement of serum albumin (odds ratio: 3.68, p = 0.027), and BMI (odds ratio: 1.235, p = 0.014) were independent predictor for successful weaning. The serum creatinine level in the 4th week remained similar in patients with daily protein intake either >1.065 g/kg/day or >1.2 g/kg/day (p = 0.5219 and p = 0.7796, respectively). Higher protein intake may have benefits in weaning in patients with PMV and had no negative impact on renal function.