Polystyrene nanoplastics (PS-NPs) are emerging environmental contaminants increasingly linked to male reproductive toxicity; however, the molecular mechanisms underlying testicular damage remain unclear. This study evaluated PS-NP-associated testicular damage in rats after 55 days of exposure and assessed the modulatory effects of
Nelumbo nucifera leaf, flower, and rhizome extracts, with quercetin as a reference. PS-NP exposure reduced spermatogenic cell populations, testicular, epididymal weights, and sperm motility. These changes were accompanied by increased
NOX4 and
NF-κB expression, upregulation of intrinsic apoptosis-related genes (
Tp53,
Bax,
Caspase-9, and
Caspase-3), elevated
caspase-3 and
caspase-9 protein levels, and enhanced cleaved
caspase-3 immunoreactivity. In contrast,
Fas and
Caspase-8 were downregulated, confirming intrinsic mitochondrial apoptosis. PS-NP exposure also altered reproductive hormone receptor expression (
LHr,
FSHr, and
AR) and dysregulated chromatin-regulatory genes, with increased
Dnmt1,
Dnmt3a, and
Ehmt2 (
G9a) and decreased
Hdac1 and
Ep300. Co-administration of
N. nucifera attenuated most of these alterations, with the rhizome extract exhibiting the most pronounced protective effect. GO and PPI network analyses suggested functional connectivity among stress-responsive, apoptotic, and chromatin-modifying proteins. Docking simulations indicated phytochemical-apoptosis-related protein interactions. PS-NPs may impair testicular homeostasis through coordinated stress, apoptosis, endocrine disturbance, and epigenetic dysregulation, with possible relevance to male reproductive health, while
N. nucifera shows promise as a protective modulator.
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