Four known metabolites, macrophin (1), rosellisin (2), 2-(2-hydroxy-5-6-methoxy-3-methylene-1,4-benzodioxin-2(3H)-one (3), and methoxyphenoxyacrylic acid (4) were isolated, for the first time, from an endophytic fungus, Phoma macrostoma inhabiting the inner tissue of medicinal plant Glycyrrhiza glabra Linn. Their structures were characterized by comparison of their NMR data with literature data, and X-ray diffraction data of macrophin (1) as described herein for the first time. The compounds (1–4) were evaluated for their growth-inhibitory activities against a panel of cancer cell lines. Of these substances, macrophin (1) showed prominent cytotoxic activity against the MDA-MB-231, T47D, MCF-7, and MIAPaCa-2 cancer-cell lines with IC50 values of 14.8, 8.12, 13.0, and 0.9 μM, respectively. This biological significance has prompted us to generate a series of five acylated analogs (1a–1e) of 1 to conduct structure–activity relationship (SAR) study. The result illustrates all the analogues (1a–1e) were more potent than 1 against MDMB-231 and MIAPaCa-2 cancer cell lines. The compound 1d, an n-butanoyl substituent, has been proven to be three-fold more potent than 1 with IC50 values of 0.3 and 3.7 µM against MIAPaCa-2 and MDMB-231 cell lines, respectively.