This study was aimed to establish a smear protocol for preparing bone marrow cells and investigate its effect on fluorescence in situ hybridization (FISH) signal. Probe DNA (C-myc, MDM2, STK6) was labeled with Spectrum Green, PromoFluor-555 and PromoFluor-415 by nick translation. Five bone marrow samples were tested by two methods separately. Traditional method: after removing the erythrocytes by hypoosmotic solution, the bone marrow cells were fixed in methanol/acetic acid (3:1). Improved method: erythrocytes were removed using density gradient centrifugation and fixed in methanol. The samples were then fixed again in 2 formaldehyde for 5 min. The FISH signal was assessed by comparing the relative signal intensity of each fluorophore with the autofluorescence background. The results indicated that improved method greatly increased the ratio of fluorescence signal intensity in the Spectrum Green, PromoFluor-555 and PromoFluor-415 channel (traditional method: 4.3 ± 0.19, 3.52 ± 0.04, 3.07 ± 0.08; improved method: 9.89 ± 0.41, 7.55 ± 0.5, 5.67 ± 0.18, n = 5, P < 0.01) respectively. The signal intensity increased 2.32, 2.14 and 1.85-fold in the Spectrum Green, PromoFluor-555 and PromoFluor-415 channel respectively. In addition, the improved method decreased the split signals [traditional method: (15.8 ± 1.74), (20.42 ± 2.88), (23.2 ± 3.02); improved method: (8.6 ± 1.2), (12.28 ± 1.33), (12.6 ± 2.56), n = 5, P < 0.05]. It is concluded that the improved optimal procedure which facilitates FISH intensity on bone marrow cells is developed, showing potential for wide application in the diagnosis of hematologic diseases.