Dietary low-fishmeal (FM) have negative impacts on growth performance and metabolic responses in aquatic animals, while Schizochytrium limacinum have multiple benefits due to its rich contents of docosahexaenoic acid (DHA). However, little information is available on the effects of S. limacinum on Pacific white shrimp (Litopenaeus vannamei) in a low-FM diet (LF). An 8-week feeding trial were used to investigate the impacts of S. limacinum on growth performance, as well as morphological changes, biochemical indicators, antioxidant capacity, and transcriptomic profiles of hepatopancreas in shrimp fed a low-FM diet. Compared to LF diet, 0.3% S. limacinum (LFLD) diet significantly decreased the specific growth rate (SGR), and did not affect the feed conversion rate (FCR) and weight gain rate (WGR); whereas 0.6% S. limacinum (LFHD) diet did not affect the SGR, FCR and WGR. Histological structures of hepatopancreas showed that LFLD and LFHD treatments reduced the number and size of secretory cells and increased the number of storage cells, compared to LF group. LFLD and LFHD diets significantly decreased the concentrations of triglyceride and total cholesterol, significantly increased the levels of glutathione peroxidase and total antioxidative capacity, while did not affect the levels of malondialdehyde and superoxide dismutase. A total of 135 differential expression genes (DEGs) were identified in LFLD group and 108 DEGs were identified in LFHD group (both compared to LF group). Administration of S. limacinum altered the transcriptomic profiles, while LFHD induced a pattern similar to that of LF. LFLD and LFHD treatments mainly affected the 9 KEGG metabolic pathways, including “Arachidonic acid metabolism” and “Glutathione metabolism”. In conclusion, LFLD treatment impaired the growth performance of shrimp, while LFHD treatment did not affect it; and both treatments improved the morphological structure, lipid accumulation and antioxidant capacity of hepatopancreas.