Abstract: Biogas slurry and residue organic fertilizer serves as an essential material carrier for chemical fertilizer reduction and efficiency enhancement, driving the green and low-carbon transformation of agriculture. However, its field fertilization is currently dominated by surface spraying, which suffers from rapid volatilization, low fertilizer utilization efficiency, and issues such as pipeline clogging, uneven fertilization due to high material viscosity during delivery, and intense sloshing impact during tank transportation. To overcome the twin technical bottlenecks of pipeline clogging for high-viscosity materials and liquid surge impacts, this study developed an intelligent biogas slurry and residue organic fertilizer applicator integrating stable delivery and active anti-clogging, and deep strip fertilization. The machine primarily consists of a suction and delivery mechanism, a surge-resistant storage tank, an active anti-clogging control system based on real-time flow feedback, and a deep strip fertilization mechanism featuring a staggered arrangement of notched rakes. Initially, the rheological characteristics of the biogas slurry and residue were characterized across representative total solid mass fractions of 2%, 4%, 6%, 8%, and 10% utilizing a rotational rheometer, which confirmed its pseudoplastic non-Newtonian fluid attributes with shear-thinning behavior. Grounded in these material properties and tailored to a tank capacity of 5m³, a specialized surge-resistant baffle plate was engineered, integrating an inverted trapezoidal wave-tooth profile and 5 vertically aligned perforated anti-surge holes. By establishing a hydrodynamic model for the liquid sloshing within the tank, the transient longitudinal sloshing force in the forward direction and the spatial displacements of the center of mass were quantitatively analyzed, providing a scientific basis for effectively mitigating wave-induced surge impacts. To accommodate the complex residue-covered soil terrain of the Northeast China black soil region, a spatial layout of staggered notched disk rake groups was designed to strengthen its residue-cutting capability and ensure a stable furrowing depth of 140–180 mm. By constructing a quasi-static mechanical model governing the rake blade-soil interaction, the core structural parameters of the rake blade were determined and verified, yielding a blade diameter of 360 mm, a blade thickness of 6 mm, and a rake assembly spacing of 420 mm. Additionally, a closed-loop active anti-clogging control system was constructed, utilizing a Siemens S7-200 SMART PLC as the core controller and an industrial-grade touchscreen human-machine interface (HMI) as the interactive terminal. The system real-time collects flow signals across the entire pipeline network through 4 groups of branch electromagnetic flowmeters. Upon detecting that the instantaneous flow rate of a specific pipeline remains below the preset threshold of 13.5 L/min for 2 consecutive seconds, the PLC immediately triggers a blockage alarm, actuates pneumatic electromagnetic valves to isolate the clogged line, and coordinates a vehicle-mounted air pump to execute a 5s high-pressure pneumatic full-length blast to thoroughly clear the deposition. Through controlled single-factor experiments and multi-factor orthogonal trials, the interactive effects of the machine forward speed and the power take-off (PTO) rotational speed on furrowing depth stability and fertilizer distribution uniformity were investigated. Range and variance analyses revealed that the tractor forward speed exerted an extremely significant influence on the coefficient of variation CV of the rake depth stability, whereas the PTO rotational speed played a dominant, extremely significant role in governing the fertilization uniformity coefficient. Ultimately, optimization parsing yielded the optimal operational parameter combination: a machine forward speed of 3 km/h combined with a PTO rotational speed of 780 r/min. Under these optimized working conditions with the active anti-clogging system continuously engaged, the entire machine demonstrated superior agronomic performance, where the CV of rake depth stability was effectively suppressed to 6.88%, and the uniformity coefficient of fertilization reached as high as 98.23%.