Soil degradation caused by watermelon continuous cropping obstacle is a serious problem in China. Compost, as a soil conditioner, has great potential in improving soil degradation. In order to explore how compost affects the soil quality under continuous cropping obstacle, associations among soil chemical characteristics, microbial community structures and agronomic variables were analyzed and compared. Results showed that soil pH, available potassium, alkali-hydrolyzable nitrogen and organic matter changed significantly after using maize straw compost and sludge compost, which indicated the feasibility of composts as soil remediations. This is also reflected on the significant changes of soil microbial community. Mizugakiibacter, as the main reason of watermelon continuous cropping obstacle, decreased significantly after using compost products. It also showed a negative connection with most chemical characteristics. Rhodanobacter and Galbibacter increased significantly after using compost products, which were positively related to most chemical characteristics. The increase of them was helpful to reduce Mizugakiibacter. Beneficial bacteria were positively related to beneficial fungi (Chaetomium and Chrysosporium). The increase of them and the decrease of Verticillium also helped to improve microbial community structure. The results indicated that compost as a useful and inexpensive technique could alleviate soil degradation caused by watermelon continuous cropping obstacle. •Soil degradation was improved after the application of compost.•Beneficial microorganism increased and harmful microorganism decreased.•Mizugakiibacter was the main reason of watermelon continuous cropping obstacle.•The increase of Rhodanobacter and Galbibacter was helpful to reduce Mizugakiibacter.•Beneficial fungi were positively related to beneficial bacteria.