Membrane-associated ring-CH-type finger 1 (MARCH1), which mediates the ubiquitination of CD86 and MHC class II proteins, plays crucial roles in ruminant fecundity. To completely explore the functions of MARCH1 in goat reproduction, the mRNA expression of this gene were investigated in different tissues of goats. Moreover, we analyzed the association of three insertions and deletions (indels) within MARCH1 with litter size in a large population of Shaanbei white cashmere goats (n = 2844). It showed that MARCH1 was expressed in all examined tissues, including the spleen, brain, lungs, liver, muscles, and testis, of 14- and 56-day-old male goats and in the ovary tissues of female goats. However, MARCH1 expression levels in the testis and lungs were significantly different between the 14- and 56-day-old male goats. Therefore, we examined MARCH1 expression levels in the testis of male goats belonging to different developmental age groups, i.e., 0-, 14-, 28-, 42-, and 56-day-old male goats. Our results indicated a potential association between MARCH1 expression and mitosis-to-meiosis transition. Furthermore, we identified three novel 7-, 15-, and 18-bp indels in MARCH1 in the Shaanbei white cashmere goat population. The presence of the three indels significantly affected MARCH1 expression in the testis and ovary. Statistical analyses indicated that these indels were associated with first-born litter size (P < 0.05). A significant difference was observed in the genotype distribution of the three indels between single- and multi-lamb female goats (P < 0.05). Together, these findings suggest that MARCH1 plays a crucial role in fertility and that the three novel indels in the goat MARCH1 can be used as effective molecular markers for marker-assisted selection of goats for breeding in the future.