Utilizing {\it ab initio} ultra-high resolution hydrodynamical simulations, we investigate the properties of the interstellar and circum-galactic medium of Ly$\alpha$ Blobs (LABs) at $z=3$, focusing on three important emission lines: Ly$\alpha$ 1216\AA, \heii 1640\AA\ and \civ 1449\AA. Their relative strengths provide a powerful probe of the thermodynamic properties of the gas when confronted with observations. By adjusting the dust attenuation effect using one parameter and matching the observed size-luminosity relation of LABs using another parameter, we show that our simulations can reproduce the observed \civ/\lya\ and \heii/\lya\ ratios adequately. This analysis provides the first successful physical model to account for simultaneously the LAB luminosity function, luminosity-size relation, and the \civ/Ly$\alpha$ and \heii/Ly$\alpha$ ratios, with only two parameters. The physical underpinning for this model is that, in addition to the stellar component for the \lya\ emission, the \lya\ and \civ\ emission lines due to shock heated gas are primarily collisional excitation driven and the \heii\ emission line collisional ionization driven. We find that the density, temperature and metallicity of the gas responsible for each emission line is significantly distinct, in a multi-phase interstellar and circumgalactic medium that is shock-heated primarily by supernovae and secondarily by gravitational accretion of gas.