Travel data collection, which is necessary for travel demand modeling, is always of great concern to modelers due to its huge cost and effort when a large sample is required to achieve satisfactory model precisions. In this paper, travel data collected based on a survey questionnaire and travelers’ active participation are called actively collected data (ACD). It is difficult to guarantee absolute randomness and unbiasedness in a sample when the ACD are collected due to self-selection issues. The aim of this study is to improve the model precision at low cost by using passively collected data (PCD), such as in-vehicle GPS data and transit smart card data, to release sample size restriction and reduce sampling bias of ACD in a commute mode choice model. In an empirical study, a multinomial-logit-based joint model is developed for commute mode choice by integrating ACD and PCD based on the choice-based sampling theory. A comprehensive set of explanatory variables are specified through data integration. Both simulation and empirical results show great improvement in coefficient precisions in the proposed joint model, relative to those in the ACD model and PCD model. In this study, ACD and PCD samples of Shanghai are integrated in the joint model so that several significantly influential level-of-service attributes are identified for auto, rail, and bus modes, and their impacts on commute mode choice probabilities are quantified. The findings can aid in better evaluating the program to improve the existing transit system.