We analyzed the effect of alliin on the recovery of mouse testicular function and structure following estradiol treatment as well as on apoptosis regulation. During the cultivation of testicular cells, high-concentration estradiol suppressed Casp-3; PCNA, mTOR, and PI3K signaling increased; and cell proliferation in the testes was abnormally increased. Therefore, estradiol treatment increased the proportion of abnormal cells. The estradiol and 2.5 μM of alliin treatment increased Casp-3 levels and suppressed Bcl-2, PCNA, mTOR, and PI3K expression. Additionally, treatment with estradiol caused tissue loss. Furthermore, Ca2+ deposition decreased, TNF-r protein expression increased, and the levels of other protein markers of cell survival and death decreased. Tissue recovery and restoration of the testes occurred after alliin treatment; the gene expression of cell survival and death markers, except for TNF-r, increased with increasing Ca2+ deposition. Cell proliferation and tissue reorganization may correlate with an increased signal of intrinsic apoptosis owing to increased Ca2+ deposition. Therefore, treatment with alliin may regulate the apoptosis of cells with normal or abnormal signal transduction and help to revert testicular dysfunction.