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Making sure communications stay safe in Non-Terrestrial Networks (NTNs) has become harder, mainly because cyber-physical attacks keep getting more advanced. Usual hardware-in-the-loop validation, it often complicates the testing process because it’s pricey, not very adaptable, and scalability constraints. To deal with that, we present the Smart Satellite Communication System (SSCS). This system is a wholly software-based, hardware-free simulation platform, designed to assess space-to-ground link resilience under complex, multi-layer threats. At the physical layer, the approach pairs an SGP4 orbital propagator using dynamic tracking loops to monitor Low Earth Orbit (LEO) passes and constantly adjusting for ±100 kHz changes in Doppler frequency.. For threat recognition, an unsupervised isolation forest model uses rolling amplitude variance features, converting that into intelligence for detecting organized electronic warfare jamming. Overall results show an AUC of 0.991. The model's accuracy is 91%. It also whitelists 697 out of 700 baseline communication frames, accomplishing that cleanly with no earlier threat signatures. On the cryptographic side, the simulation runs a BB84 Quantum Key Distribution (QKD) protocol, linking free-space optical photon loss to the Quantum Bit Error Rate (QBER) directly. When intercept-resend wiretapping is active, the observed QBER settles around 25% to 28% , which in practice is like performing a cryptographic cache purge at a 15% threshold. By monitoring both of these variable’s side by side, the system effectively separates the harmless weather-like rain fade (when QBER<10%) from the more questionable listening in behavior (QBER >20%) that is suspicious.Finally, SSCS runs on an async FastAPI ASGI arrangement, with full duplex WebSockets, so the end-to-end processing latency stays under 3 ms, even while the stress tests are handling about 5,000 packets per second.