One pair of novel enantiomers, gigantdioxin A (+)-1 and B (−)-1, with a skeleton of benzo[d][1,3]dioxin; a new acetophenone gigantone A (3); a known 3-chlorogentisyl alcohol (2), which is the bioprecursor of 1; acetophenone (4); and chromone derivative (5) were obtained from the sponge-associated fungus Aspergillus giganteus MA46-5. Their structures were established by extensive and in-depth spectral analysis, such as UV, 1D and 2D NMR, and HRESIMS. The absolute configurations of (±)-1 were deduced by ORD, chiral separation, and experimental and computational ECD. Meanwhile, we proposed a possible biosynthetic pathway of (±)-1. Fortunately, the pathway was proved by biomimetic synthesis through 2, as a bioprecursor, reacted with n-butyraldehyde. Myocardial protection assays showed that 3 and 4 possessed stronger protective effects than a positive control against myocardial cell H9c2 ischemia–reperfusion injury in low concentrations, and the effect of (−)-1 was almost equal to that of the positive control. Further, we explored the possible mechanism of myocardial protection through network pharmacology. Adenosine A2a receptor (ADORA2A) and serum albumin (ALB) represent potential targets for myocardial protection associated with (−)-1 and 4, respectively. Based on the network pharmacology, we docked the predicted proteins with bioactive compounds using Autodock Vina.