Electrolytic manganese slag (EMR) is a solid waste generated in the manganese hydrometallurgy process. It not only takes up significant land space but also contains Mn2+, which can lead to environmental contamination. There is a need for research on the treatment and utilization of EMR. Improved EMR substrate for Pennisetum sinese Roxb growth was determined in pot planting experiments. The study tested the effects of leaching solution, microorganisms, leaf cell structures, and growth data. Results indicated a substrate of 45% EMR, 40% phosphogypsum, 5% Hericium erinaceus fungi residue, 5% quicklime, and 5% dolomite sand significantly increased the available phosphorus content (135.54 ± 2.88 μg·g−1) by 17.95 times, compared to pure soil, and enhanced the relative abundance of dominant bacteria. After 240 days, the plant height (147.00 ± 0.52 cm), number of tillers (6), and aerial dry weight (144.00 ± 15.99g) of Pennisetum sinese Roxb increased by 5.81%, 200%, and 32.58%, respectively. Analyses of leaves and leaching solution revealed that the highest leaf Mn content (46.84 ± 2.91 μg·g−1) being 3.38 times higher than in pure soil, and the leaching solution Mn content (0.66 ± 0.13 μg·g−1) was lowest. Our study suggested P. sinese Roxb grown in an improved EMR substrate could be a feasible option for solidification treatment and resource utilization of EMR.