Diaporindenes A-D (1-4), four unusual 2,3-dihydro-1 H-indene isomers, a novel isoprenylisobenzofuran A (5), two new isoprenylisoindole alkaloids diaporisoindoles D and E (6 and 7), and a new benzophenone derivative tenellone D (11), together with four known biogenetic agents (8-10 and 12), were all separated from the endophytic fungus Diaporthe sp. SYSU-HQ3 guided by ultraperformance liquid chromatography high-resolution mass spectrometry. The absolute configurations of 1-7 and 11 were defined by X-ray diffraction, quantum chemical calculations, and spectroscopic analysis. Diaporindenes A-D (1-4) possessed an unprecedented chemical skeleton featuring a 2,3-dihydro-1 H-indene ring and a 1,4-benzodioxan moiety. All of the isolates (1-12) were tested for their inhibitory effects on the production of nitric oxide in lipopolysaccharide-induced microglial cells (RAW 264.7 cells). Compounds 1-5, 8, and 9 were found to exhibit significant inhibitory effects against nitric oxide production with IC50 values from 4.2 to 9.0 μM and SI values from 3.5 to 6.9. In addition, the structure-activity relationships of all compounds were summarized.