Chemical investigation of coastal saline soil-derived fungus Aspergillus flavipes RD-13 led to the isolation of two new seco-cytochalasins (1) and (2) along with nine known analogs. Their structures were elucidated by comprehensive spectral analysis, and the absolute configurations of these two new ones were determined through Rh2(OCOCF3)4-induced CD experiment and chemical interconversions. Moreover, the absolute configuration of a known compound named cytochalasins Z18 (3) was also determined for the first time. Structurally, compounds 1, 2 and 3 were the open ring derivatives of compounds 5, 8, and 4, respectively. All compounds were evaluated for their cytotoxic activities on A549, H1299 and H520 cells and 4 exhibited the strongest inhibitory activities towards the above cell lines with IC50 values of 0.15, 0.23 and 0.43 μg/mL, respectively. Preliminary structure-activity relationship analysis suggested the importance of macrocyclic ring in cytochalasins to confer cytotoxicity.