Background and aims: Childhood and adolescence are critical periods for linear growth and preventing stunting. Current evidence indicates that dietary protein intake in children and adolescents is often two to three times higher than the recommendations in many regions worldwide. However, few studies have focused on the association between high protein intake and linear growth and stunting in this population. We aim to investigate this association in children and adolescents aged 6 to 18 years in a population with relatively high protein consumption. Methods: We conducted a large cross-sectional study involving 3299 participants from Shenzhen, a modern metropolis of China. Protein intake, including total protein, animal protein, and plant protein, was evaluated by a food-frequency questionnaire and expressed as grams per kilogram of body weight per day (g·kg−1·d−1) and as a percentage of total energy intake (%E). The primary outcomes were body height and height-for-age Z score (HAZ). Generalized linear models and logistic regression analyses were employed to examine the associations between protein intake and outcomes. We also conducted stratified analyses across different genders and pubertal stages in the aforementioned associations. Results: The mean protein intake was 1.81 g·kg−1·d−1 (17% E). After adjusting for serum calcium, zinc, vitamin D3, vitamin A levels, birth outcomes, lifestyle, and parental characteristics, each standard deviation increase of 1 in protein intake (0.64 kg−1·d−1) is found to be associated with a −5.78 cm change in body height (95% CI: −6.12, −5.45) and a −0.79 change in HAZ (95% CI: −0.84, −0.74). Consistent results were observed when protein intake was expressed as %E or specifically as animal or plant protein. Moreover, the relationship between protein intake and linear growth remained consistent across genders in different pubertal stages, similar to that of the overall participants. Conclusions: Our findings highlight the potential hazards of high protein intake on linear growth in children and adolescents. Caution should be exercised when promoting increased protein consumption in children and adolescents who already have a high intake of protein.