Cistanche deserticola is a herbaceous plant that parasitizes deep in the roots of Haloxylon ammodendron and Tamarix ramosissima. Due to its small seed volume, high price, and the requirement that the seeds need to be attached near the roots of host plants during sowing, the mechanized sowing of Cistanche deserticola demands precise seed metering and deep sowing. According to the agronomic planting requirements of Cistanche deserticola and combined with manual sowing methods, a Cistanche deserticola seeder capable of ditching, sowing, and covering soil operations was designed and manufactured. By analyzing the stress state of the ditching cutterhead, the main structural parameters and the blade layout pattern of the cutterhead were determined. Based on the principle of constant volume of soil throwing and covering, the structural parameters of the soil guide cover were designed. Combined with finite element analysis software, modal analysis was mainly carried out on the ditching cutterhead and the main drive shaft, and the working parameters of the machine were determined. The sowing flow rate of Cistanche deserticola was matched according to the liquid spraying volume and the working speed, and the form and size range of the seed outlet were determined. Taking the blowing air pressure at the nozzle and the opening degree of the seed spraying port as experimental factors, and the coefficient of variation of sowing uniformity as the experimental index, field experiments were carried out. The results showed that when the blowing air pressure at the nozzle was 0.2MPa and the opening degree of the seed outlet was 1.5mm, the coefficient of variation of sowing uniformity was 13.50%, and the sowing depth stability coefficient was not less than 91.17%, which met the current agronomic planting requirements of Cistanche deserticola.