In order to provide early intervention for coronary artery lesion (CAL) caused by Kawasaki Disease (KD), we analyzed clinical characteristics of typical and incomplete KD cases from 1998 to 2008 in Northwest and Central China. A total of 383 patients included 298 cases of typical KD and 85 cases of incomplete KD. The morbidity of incomplete KD was 28.5%, a percentage significantly lower than that of typical KD. The occurrence of bulbar conjunctiva congestion, erythra, crissum red, film-like decrustation, lip red, rhagades, raspberry tongue, bilateral toe-end decrustation, limb sclerosis, cervical lymph nodes enlargement, agitation and irritability in incomplete KD group was lower than that in the group of typical KD (p < 0.05); however, the occurrence of unilateral toe-end decrustation, scar reappearance erythema, malaise, fatigue, liver incidence was significant higher in incomplete KD group (p < 0.05). Based on lab assays and inspection index comparisons, the incomplete KD cases whose C-reactive protein (CRP) and erythrocyte sedimentation rate (ESR) were significantly increased, had significantly higher reduction in blood platelet (PLT). Interestingly, the KD patients with CPR higher than 30 mg/L, ESR higher than 40 mm/h, hepatomegaly and IVIG ineffectiveness, had higher incidence of CAL development. Altogether, our data have indicated differential clinical characteristics between incomplete KD and typical KD, and have identified several high risk factors of KD for CAL, such as hepatomegaly.