Abstract Study question Do the morphokinetics of pronuclei in zygote associate with embryo developmental potential? Summary answer The position, distance to the central, size and fading time point of pronuclei were associated with blastocyst formation. What is known already Pronucleus is the nucleus formed by sperm or oocyte during fertilization containing the genetic material, which is important for further embryo development. We previously developed an AI-based morphology segmentation system for time-lapse imaging and it is able to capture the morphology changes and movement of pronuclei at the pixel level with high accuracy. In this study, we analysed the pixel-level morphokinetics of pronuclei with the blastocyst formation of the embryo under time-lapse incubation. Study design, size, duration The study was conducted in a university-affiliated IVF clinic from 2017 to 2019. There were 631 normal fertilized embryos with known blastulation results. They were cultured in the time-lapse incubator and taken images every 10 minutes from fertilization to embryo transfer/embryo freezing/discard. The images were extracted and the area of each pronucleus was segmented by the AI system. We reconstructed the segmented area of the pronucleus and count the morphokinetics parameters. Participants/materials, setting, methods The parameters included size, distance to the central, distance between each pronucleus, the movement pathway of each pronucleus and the fading time point. Quartiles of the parameters were divided into 25th (Q1), 50th (Q2), 75th (Q3) and 100th (Q4). In each quartile, the median of this quartile was presented with IQR. The chi-square test was used for the distribution comparison of the blastocyst formation. The FDR method was used to adjust the multi-comparison P-value. Main results and the role of chance We defined the pronucleus that was close to cortical as pn2 while the other was pn1. For the distance from each pronucleus to the zygote's geometric centroids (pn1_dist and pn2_dist), though pn1_dist did not show any significance, the pn2_dist showed a higher blastulation rate in Q2 (Q2:29.10% vs 17.90%). For the distance between the pronucleus (pn1_pn2_dist), the closer of PN got less blastocyst formation outcomes (Q1: 21.39% vs 31.44%). The results in the size of pronuclei (pn1_sz and pn2_sz) both showed that there was less blastocyst formation in small PN size (pn1_sz: Q1:19.90% vs 34.06%; pn2_sz: Q1:20.15% vs 33.19%). The duration from fertilization to pronuclei fading also had different blastulation rates. In the longest duration, there were the least blastocyst formation outcomes (Q4: 18.66% vs 35.81%). During the pn2 movement to the pn1, it might have an appropriate distance for the PN fusion. The result of the pn1_pn2_dist also showed that if the male and female pronuclei were too close (less than 14.98-17.24 μm ), the proportion of blastocyst formation was lower. If the movement of pn2 showed a decrease to the centre and then an increasing distance during development, more blastocyst formation was expected. Limitations, reasons for caution This was a retrospective and descriptive study and the end point of embryo developmental potential was blastocyst formation. The further association of the pronuclei parameters needs further endpoints to dig out. The diagnostic value of the pronucleus parameters needs further study to validate. Wider implications of the findings The pronucleus parameters are associated with blastocyst formation, which could serve as a non-invasive morphological tool to assess embryo developmental potential. Our study showed the explainable application of AI for enhancing the morphokinetics study. We believe both the pronucleus parameters and the AI tool could shed the light on embryology. Trial registration number ChiCTR1900025776