This paper introduces an improved redundant residue number system (RRNS) encoding method to enhance the reliability of information transmission in diffusive molecular communication (DMC). In addressing the 2-1 mapping issue in RRNS encoding, we propose a simplified low-mapping solution that effectively avoids the 2-1 mapping problem, thereby simplifying the decoding process. Leveraging the superior performance of the low-mapping algorithm, we further developed a direct decision algorithm that further simplifies the decoding algorithm by omitting the traditional minimum distance decision-making steps. Furthermore, this study delves into the impact of modulus selection on RRNS decoding performance and provides guidelines for optimizing code construction. Through simulation experiments on DMC channels, we have validated the effectiveness of the proposed RRNS encoding method, especially when employing binary concentration shift keying (BCSK) modulation and considering intersymbol interference (ISI). The simulation results show that the proposed encoding method not only significantly reduces the bit error rate (BER) but also fully meets the requirements of DMC systems, offering a promising new direction for the development of molecular communication technology. With these improvements, our method not only enhances the reliability of information transmission in DMC systems but also lays a solid foundation for future research and applications in molecular communication technology.