Abstract: In recent years, encoding information into digital polymers has been recognized as a promising method for information storage and has also found applications in encryption and anti-counterfeiting. However, most encryption systems for digital polymers rely on complex rules and do not focus on the encryption of the molecules themselves, and the construction and decryption of encryption systems requires a high time cost, which is not favorable for practical applications of digital polymer encryption. Herein, a new encryption mechanism that utilizes the properties of digital polymers themselves is discovered, and a series of novel binary encoded digital polyesters are synthesized by iterative exponential growth strategy, using γ-butyrolactone (γ-BL) and ε-caprolactone (ε-CL) as binary units (0 and 1). The molecular structure of each digital polyester is validated by nuclear magetic resonance (¹H-NMR) spectroscopy, size-exclusion chromatography (SEC) and matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF) mass spectrometry. Moreover, the decoding approach via tandem mass spectrometry has also been established. Results show that compared with other digital polymers, the digital polyesters have a unique “self-encryption” performance in mass spectrometry sequencing, that is, the stored binary information can only be clearly and accurately read out by in situ removal of protecting group of the carboxyl end, which can be completed in a very short time due to the high efficiency of MALDI-TOF detection. Moreover, as a biocompatible material, the digital polyester has a wide range of potential applications in information storage, anti-counterfeiting and cryptography.