Solid-state fermentation (SSF), an eco-friendly technology, has shown the high-yield ability to produce products such as biodiesel, pharmaceuticals, and enzymes. However, it has not yet demonstrated an advantage in ARA-containing lipids production. This study demonstrated that agar-supported SSF (AgSF) could induce Mortierella alpina M0223 to yield higher ARA-rich lipids than submerged fermentation (SmF), and elucidated the underlying mechanisms by the comparative transcriptome. AgSF-M0223 formed a mycelial network consisting mainly of surface (SH) and aerial hyphae (AH). The attenuated citrate cycle of SH compared to SmF was coupled with enhanced triglyceride biosynthesis, glycerophospholipid metabolism, and underlying increases in NADPH supply, prompting more glucose flux towards ARA-rich lipid synthesis. Besides, AH has high initial lipid and ARA amounts, while its primary metabolism was weakened due to nutrient scarcity, demonstrating attenuated lipid synthesis. The unique ARA and lipid synthesis characteristics of SH and AH enabled AgSF-M0223 to achieve high-yield ARA-rich lipids. By supplementing nutrients to AH through a spraying strategy and optimizing nutrients for SH, lipid yields reached 12.64 g/L comprising 70.41% ARA, 1.63 times higher than before optimization. These findings provided new insights into fungal physiology under SSF, and presented a promising eco-friendly paradigm for ARA production with advances in mechanical automation.