China has continued the economic reform and open door policy over 30 years with many great achievements, such as the second largest GDP, the largest import and export economy with the largest infrastructural investment in the world. On the other hand, the conflicts and risks the firms especially for small and medium sized manufacturing enterprises (SMEs) have faced are extremely serious and more acute due to the economy growth and increasing social wealth, especially in Yangtze River Delta, in the general context of ever increasing cost such as labour, land and higher customers’ expectations such as the quality of product. These serious problems are challenges for the competitiveness of SMEs in Yangtze River Delta. This research aims to investigate and improve the competitiveness of SMEs by the main variables such as enterprise’s resources, product’s competitive issues and innovation activities related barriers. To achieve the aim, the research employed a mixed method of quantitative and qualitative approaches to build the competitiveness’s belief network model by Bayesian Belief Networks and analyze the factors of the most important variables by the SPSS software. Secondly, 36 entrepreneurs of small and medium sized manufacturing enterprises in Yangtze River Delta have been carefully selected to participate in the questionnaire survey and face to face interviews. All participants are entrepreneurs who have run enterprise for at least three years. Five kinds of resources, competitive issues and innovation have been identified as the variables of competitiveness. The findings of research are mainly related to the three aspects which are general view of variables; barriers to innovation activity and importance of variables for improving the competitiveness; and the factor analysis of quality management practices. Firstly, the general condition of financial resource is the worst in resource sector of SMEs; Dependability is the best performance in competitive issues of SMEs; Lack of finance is generally identified the biggest barrier to innovation of SMEs. Secondly, the Physical resource in resource sector and Quality in competitive issues sector are the most important variables for improving the competitiveness of SMEs after BBN assessment; Lack of technical experts is the most serious barrier when the SMEs are really focusing on the innovation according to the BBN assessments. Thirdly, the factor analyses have identified the key independent factors explaining the quality management practices in these SMEs. Finally, these findings can help the SMEs build variables’ impact tables based on the outputs from the conditional assessment of BBNs to make more efficient and effective decisions when they try to improve the enterprise competitiveness, with detailed recommendations. At the same time, the importance and factors of good quality management practices have also been argued to help the entrepreneurs improve the quality performance and their enterprise competitiveness.