The likely effects on car commuters of enforcing congestion charging using the link-based corridor method include that they may shift to public transport, divert their route of travel, or decide not to travel to the related area. However, most recent research has focused mainly on the choice of modes. This paper examined the travel choices of private car commuters resulting from the congestion charging scheme set to be implemented in Jakarta, Indonesia. The scheme is intended to replace the current odd-even strategy. It is imperative to study all possible mutually exclusive alternatives faced by car commuters. A web-based e-survey was used for data collection, employing the stated preference method. The discrete choice multinomial logit model was chosen to analyze the data. A total of 401 of the 2125 respondents to the e-survey questionnaire link, evenly distributed to all areas of Greater Jakarta, were sampled in this study. The sample respondents who traveled by car, passing through the eight designated corridors, were analyzed. NLOGIT6 software was used to analyze the parameter of attributes, the probability of alternatives chosen, and the marginal effects of congestion charging on such corridors, employing the multinomial logit model (MNLM). One surprising finding was that the load factor and taxi fares were not significant, indicating that the level of in-vehicle overcrowding is not a concern of respondents, and taxi services are not a substitute for car travel. Another surprising finding was that income variables and job type do not significantly influence travel behavior. In terms of the probability of commuters to continue to travel by car when link-based congestion charging is imposed, only around half of the car travelers were willing to pay the congestion levy and pass through congestion charging corridors. The probability of car travelers diverting onto alternative roads is high, i.e., around 16.82% to 22.88%, while the probability of car travelers shifting to mass transportation is 17.69%. When interpreting direct marginal effects, there is a change in the probability of all travelers choosing to use private cars through the congestion charging corridor of −0.0338, or a decrease of −3.38% for every IDR 1000 increase in the congestion charging levy rate, ceteris paribus.