Using 48 apple germplasm resources, including diploids, triploids, and tetraploids, as experimental materials, 14 phenotypic traits of their floral organs were observed and data were collected. The distribution frequencies and coefficients of variation of different phenotypic traits were calculated and analyzed. The number and morphological characteristics of pollen grains were observed under an optical microscope, aiming to provide a reference basis for the evaluation, identification, and utilization of apple polyploid germplasm resources. The results are as follows: (1) The phenotypic diversity of floral organs in apples with different ploidies was abundant. The types of pink flower buds, yellow anthers, petals with an adjacent relative position, ovate petals, and pubescence at the base of the style union had the highest proportions, corresponding to 60.4%, 100%, 54.2%, 79.2%, and 97.9% of the distribution frequencies of the descriptors, respectively. (2) Traits such as the number of flowers per inflorescence, the number of stamens, petal length, petal width, corolla diameter, and the number of stigmas showed relatively small variations among different apple varieties (lines) of the same ploidy, with coefficients of variation all lower than 20.0%. However, among apples of different ploidies, the average values of the corolla diameter, petal length, and petal width of polyploids were significantly larger than those of diploids. The average corolla diameter of the two tetraploid varieties was also higher than that of triploids. This indicates that a larger corolla diameter, that is, larger flower size, can serve as an auxiliary indicator for asexual variation of polyploids within the same variety (line). (3)The proportion of pollen grains of different shapes varies among different ploidy varieties. The proportion of larger pollen grains, round pollen grains and square pollen grains in polyploids is significantly higher than that in diploids. The proportion of square pollen grains in triploids and tetraploids is more than ten times that in diploids. This indicates that the presence of a higher proportion of round and square pollen grains can be used as an effective auxiliary selective trait for identifying apple polyploid variations. By calculating the ratio of the number of triangular pollen grains to the sum of the number of round and square pollen grains, it was found that there is a significant difference between diploid and tetraploid varieties (lines), and a ratio of 1.6 can be used as the critical value for identifying ploidy.