L3 skeletal muscle index (L3SMI) was reportedly related to postoperative outcomes. We aimed to investigate the value of L3SMI in evaluating preoperative nutritional risk and long-term prognosis in colorectal cancer (CRC) patients. We retrospectively enrolled 400 CRC patients who underwent surgery from January 2012 to December 2014. The L3SMI was calculated by preoperative computed tomography (CT) and classified into two groups by gender quartile method. We found that the CT diagnostic criteria of sarcopenia in South China population was: male ≤38.89cm2/m2, female ≤33.28cm2/m2. Multivariate logistic regression analysis showed that low L3SMI was an independent risk factor for preoperative nutritional risk (p < 0.001). Kaplan-Meier survival curves showed that low status group had significantly lower disease-free survival (p = 0.004) and overall survival (p = 0.001), especially in TNM II stage. Multivariate Cox regression analysis revealed preoperative low L3SMI adversely affected disease-free survival (p < 0.001, HR 1.894 (95% CI: 1.330-2.698)), and overall survival (p < 0.001, HR 2.030 (95% CI: 1.420-2.902)). In conclusion, L3SMI is a useful supplement for screening preoperative nutritional risk and diagnosing sarcopenia, and a potential clinical indicator that can be used to predict the prognosis of CRC patients, especially TNM stage II patients.