Purpose: Children with borderline intelligence have difficulty with phonological awareness and decoding. This study aims to examine the spelling abilities of borderline and typical children and determine their difference in spelling abilities after an intervention with a phonological knowledge-based spelling program. Methods: The study subjects were four borderline-intelligent children and four normal-intelligent children in the third and fourth grades of elementary school whose teachers or parents reported having no sensory impairment, had an error variance of -1 SD or less on a phonological knowledge-based listening and writing test, and had normal reading achievement and reading cognitive processing skills according to RA-RCP. Results: This study showed that improving spelling knowledge through phonological knowledge-based writing intervention is possible. In particular, the phonological fluctuation score and spelling error rate of borderline intellectual children decreased significantly after the intervention, proving the effectiveness of the intervention. The phonological knowledge-based writing intervention had a positive effect on both borderline and typical children, but the gap between borderline and typical children was not completely closed. Intelligence and vocabulary significantly impacted the development of phonological knowledge, while age had no significant correlation. Conclusions: In terms of phonological manipulation skills, typically developing children performed well on phonological manipulation tasks. With delayed responses, children with borderline intelligence showed limited performance on these tasks. When it came to understanding phonological rules, typically developing children consistently processed rule-based spelling and pronunciation, while borderline children were limited to simple rule application and had difficulty handling complex variation.