Objective This study aimed to analyze the clinical factors related to the failure of autologous bone marrow mononuclear cells grafting (BMMCG) following core decompression (CD) in early stage osteonecrosis of the femoral head (ONFH). Methods In total, 148 patients (192 hips) underwent CD with autologous BMMCG for treatment of non-traumatic ONFH. The patients were classified by their ARCO staging and China-Japan Friendship Hospital (CJFH) typing system. All patients were clinically and radiographically followed up every three months during the first year and every six months in the following years. The clinical evaluation was conducted by pre- and post-operative Harris hip scores (HHS), while serial anteroposterior (AP) and frog lateral radiographs were used for post-operative radiographic evaluation. Results There were 56 hips as clinical failure cases, and 50 hips (89.29%) of failure cases developed between three and ten months after operation. Based on CJFH classification system, type L2 showed more failure rate with 60.0% (9 of 15). The Cox risk model showed that disease type was an independent risk factor for post-operative clinical failure (P = 0.042). Multivariate analysis of the Cox proportional-hazards model showed that type L1 had a hazard ratio (HR) of 0.286 (95% CI 0.100-0.816), type L3 with HR of 0.245 (95% CI 0.079-0.759), respectively. Conclusion Disease type is an important risk factor for autologous BMMCG combined with CD, and the degree of lateral pillar necrosis is a significant reference index for prognosis evaluation in early stage of ONFH.