Objective Quality control procedure based on the patient data in clinical chemistry was set up in laboratory information system (LIS). Methods Clinical chemistry tests results of outpatients and inpatients were collected from January 2016 to March 2017 in Zhejiang Provincial People's Hospital. Statistical results of daily patient data, including Xˉ, P2.5, P5, P10, P25, P50, P75, P90, P95 and P97.5 were calculated. Secondly, cumulative coefficients of variation (CV) of these statistical datawere calculated and compared to different criterions. Optimal analytes and related control concentrations were chosen. The minimum number of patient sample which use Xˉ as control point was calculated by PASS 11.0 software. Finally, the quality control procedure was set up base on the LIS and was verified by patient data. Results In outpatients, Xˉwas chosen as control point in AFU, APOA, APOB, CA, CL, HDL, K, MG, NA, NEFA, TP and URIC and the minimum number of sample needed were 23, 23, 30, 8, 10, 24, 34, 8, 8, 20, 13 and 22. P25 was chosen in ALP and TBIL. P50 was chosen in AST, GLU, GPDA and PHOS.P75 was chosen in ALB, CHE, CREA and DBIL. In inpatients, Xˉ was chosen as control point in AFU, ALB, APOA, APOB, CA, CL, HDL, K, Lpa, MG, NA, NEFA, TP and URIC and the minimum number of sample needed were 73, 19, 34, 18, 10, 30, 36, 21, 87, 12, 17, 51, 26 and 52;P25 was chosen in ALP, ALT, AST, CREA, DBIL, LDH, TBIL and TG. P50 in PHOS, P75 in GPDA, and P90 in CHE. 200 samples were needed in the tests which used percentiles as control points. Most CVs of these control points were higher than the commercial quality control used every day. Finally, a quality control procedure based on patient data were set up in LIS. L-J and Z score charts were used to find out systematic bias. Conclusion Patient data used in internal quality control was an economical and practical way, which can make up for the deficiency of traditional method.