Aim To investigate the relationship between serum proprotein convertase subtilisin/kexin type 9 (PCSK9) and small and dense low density lipoprotein cholesterol (sdLDLC) in patients with coronary heart disease (CHD). Methods From March 2014 to December 2014 in the first hospital of Shanxi Medical University, 100 patients with CHD diagnosed by coronary angiography were collected as CHD group, and 67 healthy subjects were served as control group. Lipoprint lipoprotein analyzer was used to measure the LDLC particle size, sdLDLC particle number and the percentage of sdLDLC in LDLC (sdLDLC percentage). Serum PCSK9 level was detected by enzyme-linked immunosorbent assay. Results Compared with the control group, LDLC particle size decreased (264.07±6.78 vs. 267.37±5.15, P＜0.01), sdLDLC particle number increased (5.0±9.5 vs. 4.0±5.0, P＜0.05), sdLDLC percentage increased (5.95%±10.50% vs. 3.70%±5.85%, P＜0.01) in the CHD group. The serum PCSK9 level in CHD group was significantly higher than that in control group (15.48 μg/L vs. 14.95 μg/L, U＝－2.74, P＝0.006). In the CHD group, serum PCSK9 level was positively correlated with sdLDLC percentage and LDLC (r＝0.212, P＝0.034; r＝0.202, P＝0.032). Conclusion Serum PCSK9 level is positively correlated with sdLDLC percentage in patients with CHD, and the inhibition of PCSK9 can prevent CHD.