A new method for producing biomass seedling trays with cow manure was developed based on heating to above the glass transition point of the lignin in cow dung. The maize seedling tray, manufactured through heat compression molding, could potentially meet the demand for transplanting maize seedlings. A scanning electron microscope and universal testing machine were used to compare the changes in the internal structure and mechanical properties of the seedling tray before and after the seeding period through a compression molding technique at normal temperature before seeding and a heat compression molding technique after seeding. The results showed that the strength of the seedling tray was mainly derived from the mechanical setting force of the fiber laminated in the seedling tray. Meanwhile, the moisture in the seedling tray hindered the lignin from filling in the gaps between the stem fibers in cow manure, as well as it reduced the protective effect of lignin on the laminated inlay structure of the stem fibers in cow manure. Therefore, under the premise that the material could be completely filled in the mold, the study concluded that a lower moisture content resulted in better strength and water resistance of the seedling tray. As such, this study provides an idea for the functional utilization of cow manure.