This study aimed to find an indicator at three months to predict overweight and short stature at two years in small for gestational age (SGA) infants. A total of 468 SGA infants and 4642 appropriate for gestational age (AGA) infants were included. Weight and height were measured at birth, three months and two years. Logistic regression and receiver operating characteristic (ROC) curves were performed for the catch-up growth. As compared to AGA infants, the weight of SGA infants was lower and the length/height was shorter at birth, three months, and two years. The weight of the catch-up group was significantly greater at birth and two years. The length/height of the catch-up group was greater at three months and two years. Trajectories of weight standard deviation score (SDS) and height SDS showed that the overweight group (BMI over the 85th percentile) had a shorter length/height SDS but a higher rate of the change in weight SDS during catch-up growth. The multivariate logistic regression indicated that that height at three months was an independent factor for prediction of catch-up growth at two years. The area under curve (AUC) was 0.801 with the 95% confidence interval (CI) from 0.726 to 0.876. Therefore, height at three months can predict overweight at two years.