Purposes We aimed to identify the contributing predictors for short stature and pre-shortness in Chinese preschool-aged children, and further to construct nomogram prediction models. Methods A large cross-sectional, kindergarten-based study was conducted during September-November, 2019 in Beijing. Utilizing a stratified random sampling method, total 20 kindergartens with 7310 children with complete data were eligible for analysis. Results The prevalence of short stature and pre-shortness was 3.0% (n = 222) and 11.6% (n = 848), respectively. Six contributing predictors were significantly associated with short stature, including parental height (odds ratio, 95% confidence interval, P: 0.773, 0.69-0.86, <0.001), maternal height (0.723, 0.64-0.82, <0.001), birthweight (0.826, 0.74-0.92, 0.001), birth height (0.831, 0.69-1.00, 0.046), children body mass index (1.204, 1.43-1.82, <0.001), and maternal age at menarche (1.614, 1.43-1.82, <0.001). Seven significant contributing predictors were found for pre-shortness, including parental height (0.805, 0.76-0.85, <0.001), maternal height (0.821, 0.77-0.87, <0.001), birthweight (0.881, 0.83-0.93, <0.001), birth height (0.86, 0.78-0.95, 0.003), gestational weight gain (0.851, 0.77-0.94, 0.002), children body mass index (1.142, 1.05-1.24, 0.002), and chronic disease (4.016, 1.66-9.70, 0.002). The nomogram models for short stature and pre-shortness had descent prediction accuracies. Conclusions Our findings indicate that short stature is predominantly determined by inherited and natal factors, and pre-shortness is additionally by modifiable factors.