Natural superabsorbent polymers (SAPs) were essential coating materials for developing slow-release fertilizers (SRFs) due to low cost and biodegradability. However, conventional natural SAPs were unsuitable for rice systems due to low stability and short slow-release period. Herein, a natural SAP with a semi-interpenetrating polymer network was prepared by poly (γ-glutamic acid) (PGlu), diatomite, and pullulan polysaccharide and combined with biochar to develop double-layer co-coated slow-release urea for rice systems. The results indicated that diatomite and pullulan modification significantly improved the slow-release capacity of SAP, with a significant increase in the average fertilizer 15N content of the soil profile by 37.9 ± 7.4% in 14–56 days. The improved slow-release capacity had significant benefits for the sustainability of the rice system, which increased plant N uptake by 17.2 ± 4.8%, decreased fertilizer N losses by 30.4 ± 7.2%, and increased rice grain yield by 9.88 ± 3.6%. More importantly, this natural SAP was fully degradable and its decomposition products are large amounts of small-molecule nutrients that could provide additional C, N, and Si to rice. Therefore, novel co-coated SRF may emerge as a greatly promising candidate for future intensive paddies.