This document presents Universe OS, a revolutionary cross-scale numerical simulation framework designed to unravel cosmic mysteries and address longstanding limitations in computational science, such as poor numerical stability, inadequate energy conservation, and fragmented multi-domain solvers. As a free, open-source tool for global scientists, it offers a one-to-one microcosm model of the universe, enabling seamless understanding and research of cosmic phenomena. The core of Universe OS lies in its self-consistent mathematical system and forced conservation design, featuring a five-dimensional unified evolution operator that integrates spatial field quantities, energy, time, mass transport, and microscopic interactions, eliminating numerical error accumulation fundamentally. A key application module, the 2D advection-diffusion simulation (centered on the AdvectionDiffusion2D class), supports adaptive time steps, multiple boundary conditions (periodic, Dirichlet, Neumann), and high-precision numerical schemes (third-order upwind-biased reconstruction with TVD limiters, Crank-Nicolson implicit diffusion). The framework introduces an energy account (E_heat) and reality correction (Z_proxy) mechanism to ensure absolute energy conservation, while its micro-macro coupling leverages microscopic agents and Monte Carlo sampling to avoid the high cost of traditional molecular dynamics/quantum simulations. Complemented by extended components including a Flask-based RESTful observation API, adaptive time step logging, and plotting tools, Universe OS enables real-time monitoring, data analysis, and result visualization. Rigorous testing (boundary condition verification, convergence tests, energy conservation validation) and performance benchmarking confirm its reliability and efficiency. By transforming scattered disciplinary fields into pluggable modules, Universe OS shifts scientific research focus from "building solvers" to "modeling domain knowledge," ending the era of "reinventing the wheel" in computational science. It serves as a foundational tool for interdisciplinary research in fluid mechanics, astrophysics, cosmology, and particle physics, empowering scientists to explore the universe’s mysteries through high-fidelity, conservation-driven simulations.