The invention discloses a biodegradable aliphatic-aromatic copolyester composition and application thereof. The biodegradable aliphatic-aromatic copolyester composition contains the following ingredients in percentage by mass: A: 60-89% of alkyl/alkoxy side chain-containing aliphatic-aromatic copolyester, B: 10-39% of thermoplastic starch and C: 1-10% of polyalcohol, wherein the A contains the following ingredients in percentage by mass: A1: 44-60% of aromatic polyester unit, A2: 39-55% of straight-chain aliphatic polyester unit and A3: 0.3-3% of alkyl/alkoxy side chain-containing aliphatic dibasic acid ester unit. According to the biodegradable aliphatic-aromatic copolyester composition disclosed by the invention, the alkyl/alkoxy side chain-containing aliphatic dibasic acid ester unit of a specific proportioning ratio is added, so that the yield strength of manufactured films is improved, the improvement of crop and weed puncture resistance of agricultural mulching films is facilitated, and the probability of occurrence of a hole breaking phenomenon is reduced; the oxygen gas permeability is improved, and the water vapor permeability is lowered, so that the manufactured films have better heat preserving and moisture preserving effects as the agricultural mulching films.