Objectives The types of pigs with congenital anal atresia and the changes in hematological parameters and biochemistry parameters were clarified to provide basic data for subsequent studies. Methods Clinical diagnosis or anatomical observation were conducted on 43 large white pigs with congenital anal atresia to determine the types of anal atresia. The body weight of 5 pigs with rectal-urethral fistula and 5 normal control pigs (all siblings) at the ages of 1, 10, 60, 120, and 180 days was measured. The hematological parameters and biochemistry parameters at 90, 180 ages were compared. HE slices of six tissues and organs, including liver, spleen, lungs, kidneys, cerebellum, and brain were analyzed. Results There were four types of large white pigs with congenital anal atresia including anus atresia without rectal atresia, rectal-urethral fistula, rectovaginal fistula and rectal atresia. There was no significant difference in growth rate between the pigs with rectal-urethral fistula and the normal control pigs. The results of hematological parameters and biochemistry parameters did not show significant differences. The results of tissue slices showed no significant pathological changes. Conclusions There were no significant differences in growth rate, hematological parameters and biochemistry parameters, and tissue slices between the pig with rectal-urethral fistula and the normal control pig, indicating that there are no adverse health conditions.