Sacha inchi (Plukenetia volubilis) is a valuable oilseed crop with a high content of polyunsaturated fatty acids (PUFAs). However, there is a lack of in-depth understanding of the lipidomics in Sacha inchi seeds (SIDs). Saturated fatty acids occupied more than half of the proportion (59.31%) in early development, while PUFAs accounted for 78.92% at maturation. The main triacylglycerols were TAG(18:3/18:3/18:3), TAG(18:2/18:2/18:3), and TAG(16:0/18:2/18:2). The corresponding species (18:3/18:3, 18:2/18:2, and 16:0/18:2) were also the main ingredients in diacylglycerol and phosphatidic acid, indicating high PUFA composition in the sn-1 and sn-2 positions of TAG. Only LPC(18:3), LPC(18:2), and LPC(16:0) were identified in SIDs, implying that those PUFAs on the sn-2 positions of the PC(18:3/-), PC(18:2/-), and PC(16:0/-) categories were released into the acyl-CoA pool for the Kennedy pathway. Conversely, the PC(18:1/-) and PC(18:0/-) categories might be responsible for the generation of PC-derived DAG and TAG. The lipidomics data will contribute to understanding the TAG assembly in developing SIDs, especially for PUFAs.