Objective To study the efficacy of pemetrexed or fluorouracil in combination with irinotecan in the treatment of advanced colorectal cancer. Methods 68 patients with advanced colorectal cancer were selected from January 2014 to January 2016 in Qinghai Provincial People's hospital. Patients were divided into the control group and the observation group by random grouping, and 34 patients for each group. Patients in the control group were received second-line therapy with fluorouracil and irinotecan. The patients in the observation group were received second-line therapy with the combination of pemetrexed and irinotecan. After treatment, the treatment effects, adverse reactions and living conditions of two groups were compared. Results The total effective rate of the observation group was 38.24%, was higher than that of the control group 8.82% (P<0.05); the observation group's disease control rate was 76.47%, was higher than that of the control group 52.94% (P<0.05). The incidence of adverse reactions in the observation group was 200.00%, which was lower than 305.88% in the control group (P<0.05). Progression free survival time in the observation groupwas (6.81±2.31) months, was higher than the control group (3.75±1.06) months (P<0.05); the total survival time in the observation group was (14.69±4.28) month, was higher than the control group (8.76±2.27) month (P<0.05). Conclusion In the second-line treatment of advanced colorectal cancer, the application of raltitrexed combined with irinotecan treatment, could improve the total efficiency of treatment and disease control rate, reduce adverse reactions, and prolong the survival time of patients.