Pea shoots is a popular vegetable in certain regions of the world due to their unique taste and abundance of health-promoting phytochemicals. The perishable nature and susceptibility to root rot of pea shoots necessitate a new soilless production system located close to the market. This study compared the growth of pea shoots using various cultivation methods in an LED plant factory. The results showed that early topping (4 days after transplanting, ET) promoted early harvest compared to later topping (20 days after transplanting, LT) and increased the number of harvested shoots by extending the harvest time to 2.8 times, ultimately resulting in a substantial yield improvement. Moreover, the yield of ET with a lower planting density (72 plants m−2, ET-LD) was 8.7% higher than ET with a higher planting density (126 plants m−2, ET-HD). Particularly, the average shoot fresh weight (AFW) under ET-LD exceeded that of ET-HD by 48.9%. It is advisable to consider adopting ET-LD for the cultivation of pea shoots in LED plant factories. Based on ET-LD, the yield, nutritional quality, and light use efficiency of pea shoots were further explored at different stages under three levels of light intensity (50, 100, and 150 μmol m−2·s−1). Contrasted against a light intensity of 50 μmol m−2·s−1, AFW, number of harvested shoots, and total fresh yield under a light intensity of 150 μmol m−2·s−1, increased by 60.2%, 62.8%, and 165.1%, respectively. Meanwhile, AFW, photosynthetic capacity, soluble sugar and vitamin C levels in leaves, as well as light use efficiency and photon yield, initially increased and then decreased with the extension of the planting period. Among these, soluble sugar, light use efficiency, and photon yield started to decrease after reaching the maximum value at 60–70 days after transplanting. In conclusion, a light intensity of 150 μmol m−2·s−1 with a photoperiod of 16 h d−1 using LEDs, combined with early topping within a planting period of 60–70 days, proves to be suitable for the hydroponic production of pea shoots in LED plant factories.