Pistachio (Pistacia vera L.) is one of Iran’s vital horticultural products, and the late-maturing Bayazi cultivar holds significant commercial value due to its exceptional ripening time (late autumn to winter). However, the high percentage of blank nuts in this cultivar remains a major production challenge. This research was conducted with the objective of investigating the morphological characteristics of the bud, flower, and fruit and assessing their relationship with the blank nut percentage in the Bayazi cultivar. The study was executed on 30 trees (replications) over two growing seasons (2023 and 2024) based on a Completely Randomized Design (CRD). For evaluation, samples were collected from 30 mature trees at Research Station No. 2 of the Rafsanjan Pistachio Research Center. Reproductive organs were studied using a binocular microscope and tissue fixation in FAA solution. Fruits were categorized into three groups based on kernel filling: blank, half-filled, and full kernel. The percentage of each group was analyzed using Duncan’s Multiple Range Test at a 5% significance level. Results indicated that the pistil in the Bayazi female flower is short and trifurcated, and unlike other cultivars, this structure is maintained even in the mature fruit. Furthermore, cotyledon anomalies were observed in over half of the embryos. The blank nut percentage in the two study years (2023 and 2024) was 41% and 67%, respectively. The significant increase in blankness in the second year coincided with more than 45 days of temperatures exceeding 40 °C. The findings suggest that embryonic morphological weakness and severe heat stress during the kernel filling period are the main factors contributing to blankness in this cultivar, necessitating careful management of environmental stress during this critical phase.