Manure is essential for integrating crop and livestock systems, but intensive farming has led to a mismatch between massive manure output and its proper use. In China, about 4 billion tons are produced yearly, and raw manure application remains common, posing risks like disease transmission, root damage, soil pollution (e.g., heavy metals, antibiotics), and greenhouse gas emissions. In contrast, well-composted manure improves nutrient supply and soil health while mitigating these risks. This review systematically compares raw and composted manure, analyzing their impacts on soil, water, and air within China’s policy framework (e.g., "Action Plan for Livestock Waste Utilization") and technical standards (e.g., GB/T 25246-2025). while delving into scientific evaluation methods for manure, efficient decomposition processes (including loose stacking, compact stacking, alternating loose-compact stacking, and enhancement techniques such as adding composite microbial agents and biochar), as well as safe application strategies. Key findings indicate that, compared to untreated manure, decomposed manure can increase nitrogen utilization efficiency by 47%, significantly boost soil organic matter (ranging from 122.5% to 354.8%) and humic acid content, and elevate the Shannon–Wiener diversity index of soil microbial communities to 5.6–6.0. Through the adoption of innovative processes such as the "1-Hour Nano-Composting Technology," the decomposition cycle can be substantially shortened, while effectively immobilizing or degrading emerging pollutants such as antibiotics and heavy metals. This paper aims to provide theoretical foundations and practical guidance for promoting the safe and efficient resource utilization of manure.