This experiment was conducted to investigate the effect of nano-fertilizer on seed germination and the first stages of bitter almond growth compared to other chemical fertilizers under saline conditions. In this regard, nuts were soaked in salt solutions of NaCl as 1, 3, and 5 ds m−1 for 48 h prior to stratification. Subsequently, the seeds were sown in perlite and treated by different concentrations of urea, ammonium sulfate, and nano-fertilizer at 0, 25, 50, and 100% for each fertilizer under different saline concentrations then stratified at 6 °C for 8 weeks. The treatments were arranged in a randomized complete block design in factorial experiment with three replicates and 25 seeds for each. Germination and first stages of growth measurements were estimated. Our results revealed that pre-treating seeds of bitter almond rootstock with 50% of nano-fertilizer under saline conditions markedly increased germination measurements, stem length and diameter, elongation of secondary and primary roots/plant, and number of secondary roots/plant relative to urea and ammonium sulfate fertilizers, thus throughout its vital role in increasing the moisture content of seed which in turn increased germination percentage and rate. Additionally, all the amount of nano-fertilizer was covered by plants via slow and continuous release of fertilizer, therefore producing stronger seedlings. Hence, we can conclude to use the nano-fertilizer nanourea modified with hydroxyapatite nanoparticles as a source for N, P, and Ca nutrients under saline conditions. © 2018, Springer Science+Business Media, LLC, part of Springer Nature.