Myocyte enhancer factor 2A (MEF2A) gene encodes a member of the myocyte enhancer factor 2 (MEF2) protein family, which involves in vertebrate skeletal muscle development and differentiation. The important function of MEF2A implies this gene is a potential candidate gene for considering association analysis between polymorphism and growth trait. Sequencing and forced-PCR-RFLP were used to analyze the polymorphisms of the MEF2A gene in 1009 cattle from three Chinese indigenous breeds. Three SNPs (C1598T, G1641A and C1734T) were detected in the cattle MEF2A gene, leading to a missense (P420L) and two silent mutations (E434 E, P465P). The frequencies of 1598CC genotype and the frequencies of allele 1598C varied from 0.884-1.000 in the analyzed population (NY, QC and JX). The genotypic and allelic frequencies of G1641A and C1734T in three populations were 0.034-1.000. The C1598T was associated with body length at 6 and 12 months of cattle. The G1641A was associated with average daily gain at 12 months of cattle. And the C1734T affected the average daily gain and body weight at 6 months of cattle. Those three mutations affected the early growth and development of cattle, which could be potential molecular makers in assistant selection of cattle breeding.