This study was carried out to isolate chemical constituents from the lipid enriched fraction of Ganoderma lucidum extract and to evaluate their anti-proliferative effect on tumor cells and human umbilical vein endothelial cells (HUVECs). Ergosterol derivatives (1–14) were isolated and purified from the lipid enriched fraction of G. lucidum. Their chemical structures were established by spectroscopic analyses or by comparison of mass and NMR spectral data with those reported previously. Amongst, compound 1 was purified and identified as a new one. All the compounds were evaluated for their anti-proliferative effect on human tumor cells and HUVECs in vitro. Compounds 9–13 displayed inhibitory activity against two types of human tumor cells and HUVECs, which indicated that these four compounds had both anti-tumor and anti-angiogenesis activities. Compound 2 had significant selective inhibition against two tumor cell lines, while 3 exhibited selective inhibition against HUVECs. The structure–activity relationships for inhibiting human HepG2 cells were revealed by 3D-QASR. Ergosterol content in different parts of the raw material and products of G. lucidum was quantified. This study provides a basis for further development and utilization of ergosterol derivatives as natural nutraceuticals and functional food ingredients, or as source of new potential antitumor or anti-angiogenesis chemotherapy agent.