Four new pyrazine derivatives, namely (S,E)-1-((5-(3-hydroxy-2-(hydroxymethyl)styryl)-3,6-dimethylpyrazin-2-yl)methyl)-1,3-dihydroisobenzofuran-4-ol (1), (S,E)-1-((5-(3-hydroxy-2-(methoxymethyl)styryl)-3,6-dimethylpyrazin-2-yl)methyl)-1,3-dihydroisobenzofuran-4-ol (2), (S,Z)-1-((5-(3-hydroxy-2-(methoxymethyl)styryl)-3,6-dimethylpyrazin-2-yl)methyl)-1,3-dihydroisobenzofuran-4-ol (3), and (S)-1-((5-(3-hydroxy-2-(methoxymethyl)phenethyl)-3,6-dimethylpyrazin-2-yl)methyl)-1,3-dihydroisobenzofuran-4-ol (4), together with one new 1,3-dihydroisobenzofuran derivative, (S)-2-(4-hydroxy-1,3-dihydroisobenzofuran-1-yl)acetamide (5), were isolated from the endophytic fungus Alternaria sp. HJT-Y7 collected from the leaves of Rhodiola tibetica. Their structures were determined based on extensive spectroscopic analysis and comparison of experimental and calculated electronic circular dichroism (ECD) curves. 1, 4, and 5 significantly inhibited osteoclast differentiation in RANKL-induced RAW264.7 cells and markedly restored bone mineralization in a dexamethasone-induced zebrafish osteoporosis model. These results highlight the potential of 1, 4, and 5 as promising candidates for osteoporosis therapy.