The mechanism of maternal in vivo haploid induction is not fully understood. In this study, the young embryos were identified by morphology, cytology and simple sequence repeat (SSR) markers at different developmental stages in the cross HZ514 (sweet corn) × HZI1 (inducer). The results indicated that the low seed setting rate was determined by the inducer pollen during the process of fertilization. The mosaic endosperm kernels and the different percentages of aneuploidy, mixploidy, lagged chromosome, micronuclei, chromosomal bridge and ring chromosome were found in the cross; 7.37% of the haploid embryos carried chromosome segments from HZI1. About 1% twin seedlings resulted from the cross and were analyzed by cytology and SSR markers. Four pairs of twin seedlings had different chromosome numbers (2n = 20 and 2n = 10–20) and there were some chromosome fragments from HZI1. Aneuploidy, mixploidy and the abnormal chromosomes occurred in the in vivo haploid induction by HZI1, which is the cytological basis for haploid induction and indicates that the inducer's chromosomes are prone to be lost during mitotic and meiotic divisions. Morphological, cellular and molecular evidences reveal that complete or partial chromosome elimination from inducer HZI1 controls the maize in vivo haploid induction.