Background: Millions of people are bitten by animals each year, with approximately 90% of the injuries being caused by dogs and cats. However, few studies focus on risk factors of dog- and cat-induced injury in China. Therefore, the objective of this study was to investigate the rate of dog- and cat-induced injury and its potential risk factors. Methods: The data were from a population-based cross-sectional study conducted in 2015, with a sample of 9380 children 6–19 years of age from two cities, Shenzhen (large city) and Shantou (mid-sized city), in southern China. Multivariate logistic regression models were used to identify the risk factors of injury by dogs and cats. Results: The total rates of dog and cat-induced injury were 15.1% and 8.7% during the lifetime, and 3.4% and 1.7% during the past year, respectively. Dog bites mostly occurred in the dog’s residence (49.4%). Cat scratches were more likely to be inflicted by one’s own cat (47.5%). Children living in suburban and island county had 2.83 times and 2.53 times more dog-related injuries than central urban children, respectively. After stratification by cities, injuries in Shantou were correlated with non-single child families (OR (odds ratios), 1.46; 95% CI (95% confidence interval), 1.09–1.96) and raising cats (OR, 5.34; 95% CI, 3.88–7.35). Those who disliked animals (OR, 0.62; 95% CI, 0.45–0.88) or had good academic performance (OR, 0.46; 95% CI, 0.35–0.60) had lower risk for injury. Injuries in Shenzhen were related to the mother’s educational level (OR, 1.51; 95% CI, 1.11–2.07) and mother being a migrant worker (OR, 2.10; 95% CI, 1.12–3.94). Conclusions: Family factors were important to predict dog- and cat-induced injury among children from Shenzhen, and personal factors were closely associated with injury among children form Shantou.