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Inhibitors of cytokinin oxidase/dehydrogenase (CKX) reduce the degradation of cytokinins in plants. This effect can be applied in agriculture as well as in plant tissue culture-based industries. In this work, we present the structure-activity relationship study of two series of CKX inhibitors based on diphenylurea. The compounds of Series I are derived from recently published CKX inhibitors - 3TFM-2HM and 3TFM-2HE. Here, we have identified key substituents with increased selectivity for maize ZmCKX1 and ZmCKX4a over AtCKX2 from Arabidopsis. Series II contains compounds that further excel in CKX inhibitory activity as well as in the ease of their synthesis. The best inhibitors exhibit IC50 in low nanomolar ranges with ZmCKX1 and especially with ZmCKX4a, which is generally more resistant to inhibition. The activity of the key compounds was verified in a tobacco and lobelia leaf disk assay, where N  6-isopentenyladenine was protected from degradation and promoted shoot regeneration. All prepared compounds were further tested for toxicity against Caenorhabditis elegans. The assay revealed clear differences in toxicity between compounds with and without a hydroxyalkyl group. In a broader perspective, this work increases our understanding of CKX inhibition and provides a more extensive portfolio of compounds suitable for agricultural and biotechnological research.