In order to explore the fruit traits related to the fruit cracking of pitaya (Hylocereus spp.), 279 pitaya accessions were used as test materials in this study. Genetic variation analysis, correlation analysis and multiple regression analysis were performed on 13 fruit traits including individual fruit weight, fruit longitudinal diameter, fruit transversal diameter, fruit shape index, fruit navel diameter, fruit navel depth, fruit navel shape index, skin thickness, fruit bract length in fruit navel, number of fruit bracts, fruit edible rate, soluble solid content (SSC) of central pulp, and pulp margin SSC with fruit cracking rate. The results showed that there were abundant genetic variations in 13 fruit traits and fruit cracking rate. The correlation analysis showed that the correlation coefficient between fruit cracking rate and fruit navel shape index was the largest and had a highly significant negative correlation. Fruit cracking rate was negatively correlated with fruit shape index and skin thickness, but positively correlated with edible rate and pulp margin SSC. Further multiple linear regression analysis showed that fruit navel diameter and navel depth were the two most important factors affecting fruit cracking rate, accounting for 39.30% of the variation, while other fruit traits could not significantly affect fruit cracking rate. In conclusion, the morphological structure of the fruit navel is very important to fruit cracking of pitaya, and the fruit navel shape index can be used as a key index in the breeding of cracking tolerance varieties.