Abstract: Cherry tomatoes are widely distributed in the tropical region of China. However, tomato straw waste has been massively produced, due to the extreme difficulty in collection, detoxification, and reutilization. It is urgent to efficiently, simply, and low-costly detoxify and dispose of the tomato straw waste in the conditions of relatively high temperatures and frequent rain climates. An important issue can also be focused mainly on the recycling and reutilization of plant biomass resources. The aim of this study is to compare the variation of physicochemical properties and humification under three types of covering mode: PTFE membrane, PVC membrane, and dry straw (No cover). The redundancy-correlation analysis and two-dimensional correlated Fourier transform infrared spectroscopy (2D-COS-FTIR) were conducted to elucidate the humic impact factors and the key molecular structure evolution. The result indicated that three types of covering treatments fully meet the demand of harmless thermophilic time (≥50°C and ≥5 days). The heating generation, storage, and insulation were ranked in the effective order of PTFE, None, and PVC treatment. The pH, EC, total nitrogen, total phosphorus, total potassium, and unit weight increased, as the progress of composting. Massive large granular compost was shattered to gradually increase the proportion of the small granular. The loss of total organic carbon (TOC) was reduced under the treatment of PVC membrane. The reduction rates of TOC were 20.12%, 4.63%, and 16.13%, respectively, in the PTFE, PVC, and None treatments. The PTFE treatment shared the highest humification speed, while the PVC treatment also achieved partial humification, with their humification index (HI) were 15.61%(PFTE), 9.95%(None), and 6.17%(PVC), respectively. Compared with the None cover, the PFTE treatment performed best to accelerate the humification of tomato straw. The humification was observed in the PVC treatment, while there was the lowest humification rate. 2D-COS-FTIR showed that there were the quinones, aldehydes, ketones, and polyphenols that originated from the decomposition and transformation of lignocellulose in cherry tomato straw. The amino group (from urea) was then polymerized to form the humic acid (HA), according to the composition and components of composting raw material. Besides, the large synthesis in HA might be responsible for the self-condensation of polyphenols. The covering of the membrane was promoted to accelerate the humification process. The correlation showed that the humification can be expected to positively regulate the pile's physical structure, chemical nutrients, and temperature during composting under the condition of covering PTFE and PVC membrane. The humification of cheery-tomato straw under different covering treatments can be beneficial to the optimization and development of in-site rapid straw composting.