A 26-day-old male infant presented with recurrent convulsions from 18 days of life. Laboratory investigations revealed severe hypomagnesemia (0.07 mmol/L) and hypocalcemia (1.65 mmol/L). Whole-exome sequencing was performed and identified compound heterozygous pathogenic variants in the TRPM6 gene, comprising c.5616G>A (p.Trp1872Ter) and a deletion of exons 20-23. The c.5616G>A variant was inherited from the father, and the exon 20-23 deletion was inherited from the mother; neither variant has been previously reported. Based on these findings, the diagnosis of primary hypomagnesemia with secondary hypocalcemia was confirmed. Oral magnesium sulfate supplementation was initiated, and no further convulsions occurred. At the 8-year follow-up, the patient exhibited persistent hypomagnesemia without other abnormalities. This case highlights that genetic testing helps confirm the diagnosis, and early magnesium supplementation effectively controls symptoms and prevents irreversible neurological impairment.