Abstract: Objective To investigate the molecular features of spinal muscular atrophy (SMA) related genes in SMA patients of Han nationality of southwest of China. Methods We collected 62 unrelated patients of SMA and 50 unrelated healthy individuals in this study. The copy numbers of survival motor neuron gene (SMN) and uronal-apoptosis inhibitory protein gene (NAIP) were measured by using multiplex ligation-dependent probe amplification （MLPA）. Results Of 62 patients, the copy number of SMAⅠ-Ⅳ were 30.65% (19/62), 41.94%(26/62), 16.13% (10/62), 11.29% (7/62), respectively. The deletion of SMN1 exon 7 accounts for 98.38% (61/62). The deletion of SMN1 exon 8 accounts for 82.26% (51/62). Among SMA Ⅰ patients, the homozygous deletion of NAIP exon 5 accounts for 68.42% (13/19) and heterzygous deletion accounts for 26.32% (5/19). Among SMAⅡ-Ⅳpatients, the homozygous deletion of NAIP exon 5 accounts for 13.95% (6/43) and heterzygous deletion accounts for 62.79% (27/43). Furthermore, 68.42% （13/19） patients of SMAⅠhave 1 copy and 2 copies of SMN2 gene, 84.62% (22/26) patients of SMA Ⅱ have more than 2 copies of SMN2 gene, 90.00% (9/10) SMAⅢ and 85.71% (6/7) SMAⅣ have over 2 copies of SMN2 gene and even have 5 and 6 copy of SMN2 gene. Conclusion The deletion of SMN1 gene is the main cause of SMA, and the change of SMN2 and NAIP copy number can affect the severity of SMA.