<p>In greenhouse production systems, unreasonable fertilization leads to soil degradation, nutrient loss, environmental pollution, reduced yield quality. Currently, there was still some disagreement on the impact of manure on greenhouse soil properties and yield. Therefore, in order to evaluate soil health restoration capacity of greenhouse agriculture, the present study conducted a comprehensive analysis using data from 55 global studies published before March 2023. Emphasis was given to understand the impact of manure application on soil pH, organic carbon (SOC), ammonium nitrogen (NH₄⁺-N), nitrate nitrogen (NO₃⁻-N), microbial biomass carbon (SMBC) and nitrogen (SMBN), crop yield. Results showed significance increases in SOC (19.8%), NH₄⁺-N (17.7%), SMBC (42.9%), SMBN (80.8%) and crop yield (10.9%) (<i>P</i> &lt; 0.05) on manure application over control. Among the different manure types, poultry manure (POM) application had the greatest promoting effect on SOC (54.3%), SMBC (123.3%) and crop yield (48.1%), while cow manure (CM) resulted in the highest increased greenhouse soil NO₃⁻-N (26.3%). In addition, SMBC (93.09%) and SMBN (176.05%) significantly increased under manure with nitrogen rate of 150–300&#xa0;kg ha⁻¹ (<i>P</i> &lt; 0.05). The results of structural equation models showed that SOC, NO₃⁻-N, SMBC and SMBN were the main factors explaining the variation in greenhouse crop yield. In addition, SOC had a direct (path coefficient = 0.28) or indirect (path coefficient = 0.16) effect on greenhouse crop yield. In summary, poultry manure application was more conducive to enhance SOC (54.3%) and SMBC (123.3%), thus contributing to soil carbon cycling. In order to enhance greenhouse soil microbial biomass, improve soil quality and promote sustainable development of greenhouse production systems, this study suggested the nitrogen application rate in manure of 150–300&#xa0;kg ha⁻¹.</p>