Bio-based controlled release fertilizers (BCRFs) are cost-effective and renewable thus gradually replacing petroleum-based controlled release fertilizers (CRFs). However, most of the study mainly focused on modifying BCRFs to improve controlled-release performance. It is necessary to further increase the functionality of BCRF for expanding the application. A multifunctional double layered bio-based CRF (DCRF) was prepared. Urea was used as the core of fertilizer, bio-based polyurethane was used as the inner coating, and sodium alginate and copper ions formed the hydrogel as the outer coating. In addition, mesoporous silica nanoparticles loaded with sodium selenate was used to modify the sodium alginate hydrogel (MSN@Se hydrogel). The results showed that the nitrogen longevity of the DCRF was much better than that of urea and BCRF. The selenium nutrient longevity of the DCRF was 40 h, much longer than that of sodium selenate. The DCRF improved the yield and nutritive value of cherry radish (Raphanus sativus L. var.radculus pers) with the elevated contents of selenium, an essential trace element. Moreover, the DCRF showed inhibitory effect on Fusarium oxysporum Schltdl. and could resist soil-borne fungal diseases continuously. Overall, this multifunctional fertilizer has great potential for expanding the use of BCRFs for sustainable development of agriculture.