Polycystic ovarian syndrome (PCOS) is the most principal reason for infertility in reproductive women, but no versatile treatment is feasible. Although trans-10-hydroxy-2-decenoic acid (10H2DA) exhibits the anti-inflammatory, anti-cancerous and immunomodulatory properties, its role in improving PCOS remains elusive. This present study examined the effects of 10H2DA on the estrous cycle, ovarian morphology, reproductive hormone, glucose and insulin tolerances of PCOS mice, analyzed the binding between 10H2DA and free fatty acid receptor 4 (FFAR4), and explored the regulation of 10H2DA on the c-Jun N-terminal kinase (JNK)/JUN (Jun proto-oncogene) signaling, cytosolic calcium ion (Ca2+), endoplasmic reticulum (ER) Ca2+ release, mitochondrial Ca2+, mitochondrial function, autophagy, lysosomal acidification, mitochondrial fission, secretion function and apoptosis of ovarian granulosa cells (GCs) using enzyme-linked immunosorbent assay, flow cytometry, Western blotting, molecular docking, various fluorescent probes or plasmid, etc. The results showed that 10H2DA alleviated the symptom of PCOS mice through improving the secretion dysfunction of GCs and protecting GCs against apoptosis. After binding to FFAR4 and inactivation of JNK/JUN signaling, 10H2DA restricted the release of ER Ca2+ through targeting ryanodine receptors (RYRs) which had been identified as the downstream targets of JUN, diminished cytosolic Ca2+ accumulation and prevented Ca2+ influx into mitochondria via adjusting the mitochondrial calcium uptake 1 and mitochondrial calcium uniporter. Concurrently, 10H2DA kept the integrity of mitochondrial function through maintaining mitochondrial Ca2+ homeostasis and suppressed the discharge of mitochondrial reactive oxygen species into the cytosol through blocking the mitochondrial permeability transition pore opening to avoid the lipid peroxidation and ameliorate the secretory function and apoptosis of GCs. Furthermore, 10H2DA rescued the defective autophagic flux along with the decline of autophagosomes and sequestosome 1 aggregation, restored the mitophagy flux with the abatement of mitophagosomes and Parkin recruitment to mitochondria, and accelerated the lysosomal degradation for depolarized mitochondria with the recovery of lysosomal acidification, whereas activation of JNK antagonized the amelioration of 10H2DA on above effectiveness, but this antagonism was counteracted by the attenuation of intracellular Ca2+. After application of 10H2DA, dynamin-related protein 1 phosphorylation was diminished and its recruitment to mitochondrial surface was impeded concomitant with the improvement of mitochondrial fragmentation, whereas inhibition of late-stage autophagy caused the failure of 10H2DA in improving mitochondrial fission. Collectively, 10H2DA might ameliorate PCOS mice through modulating autophagy-mediated mitochondrial fission dependent on the maintenance of Ca2+ homeostasis between ER and mitochondria.