The invention provides a 2, 6-naphthalic acid-based copolyester material and a preparation method thereof, and the structural formula of the material is composed of structural units represented by a general formula (1) and a general formula (2). The invention also provides a preparation method of the 2, 6-naphthalic acid-based copolyester material. According to the invention, 2, 6-naphthalic acid (2, 6-naphthalic acid diester compound), 2, 5-thiophenedicarboxylic acid (2, 5-thiophenedicarboxylic acid diester compound) or 2, 5-furandicarboxylic acid (2, 5-furandicarboxylic acid diester compound) and diol are subjected to direct esterification or ester exchange reaction to prepare the copolyester material, and the bio-based monomer 2, 5-thiophenedicarboxylic acid (2, 5-thiophenedicarboxylic acid diester compound) or 2, 5-furandicarboxylic acid (2, 5-furandicarboxylic acid diester compound) can easily increase the bio-based content of the 2, 6-naphthalic acid-based polyester, improve the toughness, and improve the barrier property.